Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | Friends | List of all members
core::scoring::ScoringManager Class Reference

#include <ScoringManager.hh>

Inheritance diagram for core::scoring::ScoringManager:
Inheritance graph
[legend]

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_Potentialget_RNA_DMS_Potential () const
 Get an instance of the RNA_DMS_Potential scoring object. More...
 
rna::data::RNA_DMS_LowResolutionPotentialget_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...
 

Private Attributes

VdWTinkerPotentialOP vdw_tinker_potential_
 
PairEPotentialOP pairE_potential_
 
RamachandranOP rama_
 
Ramachandran2BOP rama2b_
 
RamaPreProOP rama_pp_
 
P_AA_ABEGO3_OP paa_abego3_
 
OmegaTetherOP omega_
 
EnvPairPotentialOP env_pair_potential_
 
SmoothEnvPairPotentialOP smooth_env_pair_potential_
 
CenRotEnvPairPotentialOP cen_rot_pair_potential_
 
CenHBPotentialOP cen_hb_potential_
 
SecondaryStructurePotentialOP secondary_structure_potential_
 
std::map< std::string, AtomVDWOPatom_vdw_
 
rna::RNA_AtomVDWOP rna_atom_vdw_
 
geometric_solvation::DatabaseOccSolEneOP occ_hbond_sol_database_
 
dna::DirectReadoutPotentialOP dna_dr_potential_
 
mm::MMLJLibraryOP mm_lj_library_
 
mm::MMLJEnergyTableOP mm_lj_energy_table_
 
mm::MMTorsionLibraryOP mm_torsion_library_
 
mm::MMBondAngleLibraryOP mm_bondangle_library_
 
mm::MMBondLengthLibraryOP mm_bondlength_library_
 
dna::DNA_EnvPairPotentialOP dna_env_pair_potential_
 
dna::DNA_DihedralPotentialOP dna_dihedral_potential_
 
dna::DNABFormPotentialOP dnabform_
 
dna::DNATorsionPotentialOP dna_torsion_potential_
 
dna::DNA_BasePotentialOP DNA_base_potential_
 
carbon_hbonds::CarbonHBondPotentialOP carbon_hbond_potential_
 
std::map< std::string,
rna::RNA_LowResolutionPotentialOP
rna_low_resolution_potential_
 
rna::RNP_LowResPotentialOP rnp_low_res_potential_
 
rna::RNP_LowResPairDistPotentialOP rnp_low_res_pair_dist_potential_
 
rna::RNP_LowResStackDataOP rnp_low_res_stack_data_
 
rna::chemical_shift::RNA_ChemicalShiftPotentialOP rna_chemical_shift_potential_
 
rna::data::RNA_DMS_PotentialOP rna_dms_potential_
 
rna::data::RNA_DMS_LowResolutionPotentialOP rna_dms_low_resolution_potential_
 
std::map< std::pair< bool,
std::string >
, rna::RNA_SuitePotentialOP
rna_suite_potential_
 
rna::TNA_SuitePotentialOP tna_suite_potential_
 
std::map< std::string,
loop_graph::evaluator::SixDTransRotPotentialOP
loop_close_six_d_potential_
 
std::map< std::string,
utility::pointer::shared_ptr
< std::string > > 
nmer_svm_list_file_contents_map_
 
std::map< std::string,
utility::libsvm::Svm_rosettaOP > 
nmer_svm_map_
 
std::map< std::string,
utility::pointer::shared_ptr
< std::string > > 
nmer_svm_rank_list_file_contents_map_
 
std::map< std::string,
utility::pointer::shared_ptr
< utility::vector1< core::Real > > > 
nmer_svm_rank_map_
 
std::map< std::string,
utility::pointer::shared_ptr
< std::map< core::chemical::AA,
utility::vector1< core::Real > > > > 
nmer_pssm_map_
 
std::map< std::string,
utility::pointer::shared_ptr
< std::map< char,
utility::vector1< core::Real > > > > 
nmer_svm_aa_matrix_map_
 
std::map< std::string,
utility::pointer::shared_ptr
< std::list< std::string > > > 
mhc_matrix_contents_map_
 
std::map< std::string,
utility::pointer::shared_ptr
< std::pair< std::map
< std::string, core::Real >
, core::Size > > > 
mhc_sqlite_db_contents_map_
 
std::map< std::string,
utility::pointer::shared_ptr
< std::list< std::string > > > 
mhc_csv_db_contents_map_
 
P_AAOP p_aa_
 
P_AA_ssOP p_aa_ss_
 
WaterAdductHBondPotentialOP water_adduct_hbond_potential_
 
GenBornPotentialOP gen_born_potential_
 
HydroxylTorsionPotentialOP hxl_tors_potential_
 
MultipoleElecPotentialOP multipole_elec_potential_
 
SASAPotentialOP sasa_potential_
 
FACTSPotentialOP facts_potential_
 
GenericBondedPotentialOP generic_bonded_potential_
 
disulfides::FullatomDisulfidePotentialOP fa_disulfide_potential_
 
disulfides::CentroidDisulfidePotentialOP cen_disulfide_potential_
 
disulfides::DisulfideMatchingPotentialOP disulfide_matching_potential_
 
MembranePotentialOP membrane_potential_
 
membrane::MembraneDataOP mp_base_potential_
 
Membrane_FAPotentialOP membrane_fapotential_
 
ProQPotentialOP ProQ_potential_
 
PointWaterPotentialOP pwp_
 
PoissonBoltzmannPotentialOP PB_potential_
 
SplitUnfoldedTwoBodyPotentialOP sutbp_
 
UnfoldedStatePotentialOP unf_state_
 
carbohydrates::CHIEnergyFunctionOP CHI_energy_function_
 
carbohydrates::OmegaPreferencesFunctionOP carbohydrate_omega_preferences_function_
 
nv::NVlookupOP NV_lookup_table_
 
orbitals::OrbitalsLookupOP orbitals_lookup_table_
 
interface_::DDPlookupOP DDP_lookup_table_
 
std::map
< etable::EtableOptions,
etable::EtableOP
etables_by_options_
 
std::map< std::string,
etable::MembEtableOP
memb_etables_
 
core::scoring::elec::CPRepMapTypeOP cp_rep_map_byname_
 Cached data used by FA_ElecEnergy with beta_nov15. More...
 
std::map< std::string,
core::scoring::aa_composition_energy::AACompositionEnergySetupOP
aa_composition_setup_helpers_
 Cached data used by the AACompositionEnergy. More...
 
std::map< std::string,
core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP
mhc_epitope_setup_helpers_
 Cached data used by the MHCEpitopeEnergy. More...
 
std::map< std::string,
core::scoring::netcharge_energy::NetChargeEnergySetupOP
netcharge_setup_helpers_
 Cached data used by the NetChargeEnergy. More...
 
std::map< std::string,
core::chemical::mainchain_potential::MainchainScoreTableOP
rama_prepro_mainchain_potentials_
 Cached mainchain torsion potentials, used by rama_prepro. More...
 
std::map< std::string,
core::chemical::mainchain_potential::MainchainScoreTableOP
rama_prepro_mainchain_potentials_beforeproline_
 Cached mainchain torsion potentials, used by rama_prepro. More...
 
utility::vector1
< methods::EnergyMethodCreatorOP
method_creator_map_
 The map of ( score type enum -> EnergyMethodCreatorOP ). More...
 

Friends

class utility::SingletonBase< ScoringManager >
 

Constructor & Destructor Documentation

core::scoring::ScoringManager::ScoringManager ( )
private
core::scoring::ScoringManager::~ScoringManager ( )
privatedefault

Member Function Documentation

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.

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

References create_memb_etable_instance_silly(), and memb_etables_.

core::scoring::aa_composition_energy::AACompositionEnergySetupOP core::scoring::ScoringManager::create_aa_composition_energy_setup_instance ( std::string const &  filename)
staticprivate

Create an instance of an AACompositionEnergySetup object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_cloned_aa_comp_setup_helpers().

AtomVDWOP core::scoring::ScoringManager::create_atomvdw_instance ( std::string const &  atom_type_set_name)
staticprivate

Create an instance of the AtomVDW object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_AtomVDW().

carbon_hbonds::CarbonHBondPotentialOP core::scoring::ScoringManager::create_carbon_hbond_potential_instance ( )
staticprivate

Create an instance of the CarbonHBondPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_CarbonHBondPotential().

CenHBPotentialOP core::scoring::ScoringManager::create_cenhbpotential_instance ( )
staticprivate

Create an instance of the CenHBPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_CenHBPotential().

CenRotEnvPairPotentialOP core::scoring::ScoringManager::create_cenrotenvpair_instance ( )
staticprivate

Create an instance of the CenRotEnvPairPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_CenRotEnvPairPotential().

disulfides::CentroidDisulfidePotentialOP core::scoring::ScoringManager::create_centroid_disulfide_potential_instance ( )
staticprivate

Create an instance of the CentroidDisulfidePotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_CentroidDisulfidePotential().

carbohydrates::CHIEnergyFunctionOP core::scoring::ScoringManager::create_chi_energy_function_instance ( )
staticprivate

Create a (default) instance of the CHIEnergyFunction object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.

References core::scoring::TR().

Referenced by get_CHIEnergyFunction().

geometric_solvation::DatabaseOccSolEneOP core::scoring::ScoringManager::create_database_occsolene_instance ( std::string const &  atom_type_set_name,
core::Real const &  min_occ_energy 
)
staticprivate

Create an instance of the DatabaseOccSolEne object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DatabaseOccSolEne().

interface_::DDPlookupOP core::scoring::ScoringManager::create_ddp_lookup_instance ( )
staticprivate

Create an instance of the DDPlookup object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DDPLookupTable().

disulfides::DisulfideMatchingPotentialOP core::scoring::ScoringManager::create_disulfide_matching_potential_instance ( )
staticprivate

Create an instance of the DisulfideMatchingPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DisulfideMatchingPotential().

dna::DNABFormPotentialOP core::scoring::ScoringManager::create_dna_bform_potential_instance ( )
staticprivate

Create an instance of the DNABFormPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DNABFormPotential().

dna::DNA_DihedralPotentialOP core::scoring::ScoringManager::create_dna_dihedralpotential_instance ( )
staticprivate

Create an instance of the DNA_DihedralPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DNA_DihedralPotential().

dna::DirectReadoutPotentialOP core::scoring::ScoringManager::create_dna_directreadoutpotential_instance ( )
staticprivate

Create an instance of the DirectReadoutPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DirectReadoutPotential().

dna::DNA_EnvPairPotentialOP core::scoring::ScoringManager::create_dna_envpairpotential_instance ( )
staticprivate

Create an instance of the DNA_EnvPairPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DNA_EnvPairPotential().

dna::DNATorsionPotentialOP core::scoring::ScoringManager::create_dna_torsion_potential_instance ( )
staticprivate

Create an instance of the DNATorsionPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DNATorsionPotential().

dna::DNA_BasePotentialOP core::scoring::ScoringManager::create_dnabase_potential_instance ( )
staticprivate

Create an instance of the FactsPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_DNA_BasePotential().

EnvPairPotentialOP core::scoring::ScoringManager::create_envpairpotential_instance ( )
staticprivate

Create an instance of the EnvPairPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_EnvPairPotential().

etable::EtableOP core::scoring::ScoringManager::create_etable_instance ( etable::EtableOP  table_in)
staticprivate

Create an instance of an Etable, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager. This one is kind of silly, since it just returns an EtableOP that is passed in. Still needed for threadsafe creation, though.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by etable().

FACTSPotentialOP core::scoring::ScoringManager::create_facts_potential_instance ( )
staticprivate

Create an instance of the FactsPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_FACTSPotential().

utility::pointer::shared_ptr< std::string > core::scoring::ScoringManager::create_file_contents_instance ( std::string const &  filename)
staticprivate

Create an instance of the contents of a file.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::scoring::TR().

Referenced by get_nmer_svm_list_file_contents(), and get_nmer_svm_rank_list_file_contents().

disulfides::FullatomDisulfidePotentialOP core::scoring::ScoringManager::create_fullatom_disulfide_potential_instance ( )
staticprivate

Create an instance of the FullatomDisulfidePotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_FullatomDisulfidePotential().

GenBornPotentialOP core::scoring::ScoringManager::create_genborn_instance ( )
staticprivate

Create an instance of the GenBornPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_GenBornPotential().

GenericBondedPotentialOP core::scoring::ScoringManager::create_generic_bonded_potential_instance ( )
staticprivate

Create an instance of the GenericBondedPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.

Referenced by get_GenericBondedPotential().

HydroxylTorsionPotentialOP core::scoring::ScoringManager::create_hxl_potential_instance ( )
staticprivate

Create an instance of the HydroxylTorsionPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_HydroxylTorsionPotential().

core::chemical::mainchain_potential::MainchainScoreTableOP core::scoring::ScoringManager::create_mainchain_scoretable_instance ( core::chemical::mainchain_potential::MainchainScoreTableOP  table_in)
staticprivate

Create an instance of a MainchainScoreTable, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager. This one is kind of silly, since it just returns a MainchainScoreTableOP that is passed in. Still needed for threadsafe creation, though.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_rama_prepro_mainchain_torsion_potential().

etable::MembEtableOP core::scoring::ScoringManager::create_memb_etable_instance ( std::string const &  table_id)
staticprivate

Create an instance of a MembEtable, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager. This is the non-silly version that builds the object based on a string.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::FA_STANDARD, and core::scoring::FA_STANDARD_DEFAULT.

Referenced by memb_etable().

etable::MembEtableOP core::scoring::ScoringManager::create_memb_etable_instance_silly ( etable::MembEtableOP  table_in)
staticprivate

Create an instance of a MembEtable, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager. This one is kind of silly, since it just returns a MembEtableOP that is passed in. Still needed for threadsafe creation, though.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by add_memb_etable().

membrane::MembraneDataOP core::scoring::ScoringManager::create_membrane_data_instance ( )
staticprivate

Create an instance of the MembraneData object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_MembraneData().

Membrane_FAPotentialOP core::scoring::ScoringManager::create_membrane_fa_potential_instance ( )
staticprivate

Create an instance of the Membrane_FAPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_Membrane_FAPotential().

MembranePotentialOP core::scoring::ScoringManager::create_membrane_potential_instance ( )
staticprivate

Create an instance of the MembranePotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_MembranePotential().

utility::pointer::shared_ptr< std::list< std::string > > core::scoring::ScoringManager::create_mhc_csv_contents ( std::string const &  filename)
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!

Note
Not intended for use outside of ScoringManager.
Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

References core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::check_file_size(), protocols::abinitio::filename(), and core::scoring::TR().

Referenced by get_mhc_csv_contents().

core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP core::scoring::ScoringManager::create_mhc_epitope_energy_setup_instance ( std::string const &  filename)
static

Create an instance of an MHCEpitopeEnergySetup object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Chris Bailey-Kellogg (cbk@c.nosp@m.s.da.nosp@m.rtmou.nosp@m.th.e.nosp@m.du), copied from Vikram K. Mulligan's netcharge_energy

Referenced by get_cloned_mhc_epitope_setup_helpers().

utility::pointer::shared_ptr< std::pair< std::map< std::string, core::Real >, core::Size > > core::scoring::ScoringManager::create_mhc_map_from_db ( std::string const &  filename)
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!

Note
Not intended for use outside of ScoringManager.
Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

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().

utility::pointer::shared_ptr< std::list< std::string > > core::scoring::ScoringManager::create_mhc_matrix_contents ( std::string const &  filename)
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!

Note
Not intended for use outside of ScoringManager.
Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

References core::scoring::TR().

Referenced by get_mhc_matrix_contents().

mm::MMBondAngleLibraryOP core::scoring::ScoringManager::create_mm_bondangle_library_instance ( )
staticprivate

Create an instance of the MMBondAngleLibrary object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::FA_STANDARD, and protocols::hybridization::score.

Referenced by get_MMBondAngleLibrary().

mm::MMBondLengthLibraryOP core::scoring::ScoringManager::create_mm_bondlength_library_instance ( )
staticprivate

Create an instance of the MMBondLengthLibrary object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::FA_STANDARD, and protocols::hybridization::score.

Referenced by get_MMBondLengthLibrary().

mm::MMLJEnergyTableOP core::scoring::ScoringManager::create_mm_lj_energy_table_instance ( )
staticprivate

Create an instance of the MMLJEnergyTable object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_MMLJEnergyTable().

mm::MMLJLibraryOP core::scoring::ScoringManager::create_mm_lj_library_instance ( )
staticprivate

Create an instance of the MMLJLibrary object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::FA_STANDARD.

Referenced by get_MMLJLibrary().

mm::MMTorsionLibraryOP core::scoring::ScoringManager::create_mm_torsion_library_instance ( )
staticprivate

Create an instance of the MMTorsionLibrary object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::FA_STANDARD, and protocols::hybridization::score.

Referenced by get_MMTorsionLibrary().

MultipoleElecPotentialOP core::scoring::ScoringManager::create_multipole_elec_instance ( methods::EnergyMethodOptions const &  options)
staticprivate

Create an instance of the HydroxylTorsionPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_MultipoleElecPotential().

core::scoring::netcharge_energy::NetChargeEnergySetupOP core::scoring::ScoringManager::create_netcharge_energy_setup_instance ( std::string const &  filename)
staticprivate

Create an instance of an NetChargeEnergySetup object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_cloned_netcharge_setup_helpers().

utility::pointer::shared_ptr< std::map< core::chemical::AA, utility::vector1< core::Real > > > core::scoring::ScoringManager::create_nmer_pssm ( std::string const &  filename,
core::Size  nmer_length 
)
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!

Note
Not intended for use outside of ScoringManager.
Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

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().

utility::pointer::shared_ptr< std::map< char, utility::vector1< core::Real > > > core::scoring::ScoringManager::create_nmer_svm_aa_matrix ( std::string const &  filename)
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!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References protocols::cluster::calibur::aa, core::scoring::TR(), and protocols::hybridization::val.

Referenced by get_nmer_svm_aa_matrix().

utility::pointer::shared_ptr< utility::vector1< core::Real > > core::scoring::ScoringManager::create_nmer_svm_rank ( std::string const &  filename)
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!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References protocols::hybridization::score, protocols::sparta::split(), and core::scoring::TR().

Referenced by get_nmer_svm_rank().

nv::NVlookupOP core::scoring::ScoringManager::create_nvlookup_instance ( )
staticprivate

Create an instance of the NVlookup object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_NVLookupTable().

carbohydrates::OmegaPreferencesFunctionOP core::scoring::ScoringManager::create_omega_preferences_function_instance ( )
staticprivate

Create a (default) instance of the OmegaPreferencesFunction object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.

References core::scoring::TR().

Referenced by get_OmegaPreferencesFunction().

OmegaTetherOP core::scoring::ScoringManager::create_omegatether_instance ( )
staticprivate

Create an instance of the OmegaTether object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_OmegaTether().

orbitals::OrbitalsLookupOP core::scoring::ScoringManager::create_orbitals_lookup_instance ( )
staticprivate

Create an instance of the OrbitalsLookup object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_OrbitalsLookupTable().

P_AA_ABEGO3_OP core::scoring::ScoringManager::create_p_aa_abego3_instance ( )
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!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_P_AA_ABEGO3().

P_AAOP core::scoring::ScoringManager::create_p_aa_instance ( )
staticprivate

Create an instance of the P_AA object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_P_AA().

P_AA_ssOP core::scoring::ScoringManager::create_p_aa_ss_instance ( )
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!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_P_AA_ss().

PairEPotentialOP core::scoring::ScoringManager::create_pairE_potential_instance ( )
staticprivate

Create an instance of the PairEPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_PairEPotential().

PointWaterPotentialOP core::scoring::ScoringManager::create_point_water_potential_instance ( )
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!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_PointWaterPotential().

PoissonBoltzmannPotentialOP core::scoring::ScoringManager::create_poisson_boltzmann_potential_instance ( )
staticprivate

Create an instance of the PoissonBoltzmannPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_PoissonBoltzmannPotential().

ProQPotentialOP core::scoring::ScoringManager::create_proq_potential_instance ( )
staticprivate

Create an instance of the ProQPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_ProQPotential().

Ramachandran2BOP core::scoring::ScoringManager::create_rama2b_instance ( )
staticprivate

Create an instance of the Ramachandran2B object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

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

Referenced by get_Ramachandran2B_ptr().

RamachandranOP core::scoring::ScoringManager::create_rama_instance ( )
staticprivate

Create an instance of the Ramachandran object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_Ramachandran_ptr().

RamaPreProOP core::scoring::ScoringManager::create_ramapp_instance ( )
staticprivate

Create an instance of the RamaPrePro object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

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

Referenced by get_RamaPrePro().

rna::RNA_AtomVDWOP core::scoring::ScoringManager::create_rna_atomvdw_instance ( )
staticprivate

Create an instance of the RNA_AtomVDW object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_RNA_AtomVDW().

rna::chemical_shift::RNA_ChemicalShiftPotentialOP core::scoring::ScoringManager::create_rna_chemshiftpotential_instance ( )
staticprivate

Create an instance of the RNA_ChemicalShiftPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_RNA_ChemicalShiftPotential().

rna::data::RNA_DMS_LowResolutionPotentialOP core::scoring::ScoringManager::create_rna_dms_lowrespotential_instance ( )
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!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_RNA_DMS_LowResolutionPotential().

rna::data::RNA_DMS_PotentialOP core::scoring::ScoringManager::create_rna_dms_potential_instance ( )
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!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_RNA_DMS_Potential().

rna::RNA_LowResolutionPotentialOP core::scoring::ScoringManager::create_rna_lowresolutionpotential_instance ( std::string const &  database_file)
staticprivate

Create an instance of the RNA_LowResolutionPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Andrew M. Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

References core::scoring::TR().

Referenced by get_RNA_LowResolutionPotential().

rna::RNA_SuitePotentialOP core::scoring::ScoringManager::create_rna_suitepotential_instance ( bool const &  calculate_suiteness_bonus,
std::string const &  suiteness_bonus 
)
staticprivate

Create an instance of the RNA_SuitePotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::scoring::suiteness_bonus.

Referenced by get_rna_suite_potential().

rna::RNP_LowResPairDistPotentialOP core::scoring::ScoringManager::create_rnp_lowrespairdistpotential_instance ( )
staticprivate

Create an instance of the RNP_LowResPairDistPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Andrew Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

Referenced by get_RNP_LowResPairDistPotential().

rna::RNP_LowResPotentialOP core::scoring::ScoringManager::create_rnp_lowrespotential_instance ( )
staticprivate

Create an instance of the RNP_LowResPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_RNP_LowResPotential().

rna::RNP_LowResStackDataOP core::scoring::ScoringManager::create_rnp_lowresstackdata_instance ( )
staticprivate

Create an instance of the RNP_LowResStackData object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_RNP_LowResStackData().

SASAPotentialOP core::scoring::ScoringManager::create_sasa_potential_instance ( )
staticprivate

Create an instance of the SASAPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_SASAPotential().

SecondaryStructurePotentialOP core::scoring::ScoringManager::create_secondarystructurepotential_instance ( )
staticprivate

Create an instance of the SecondaryStructurePotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_SecondaryStructurePotential().

loop_graph::evaluator::SixDTransRotPotentialOP core::scoring::ScoringManager::create_sixdtransrotpotential_instance ( std::string const &  database_file)
staticprivate

Create an instance of the SixDTransRotPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::scoring::TR().

Referenced by get_LoopCloseSixDPotential().

SmoothEnvPairPotentialOP core::scoring::ScoringManager::create_smoothenvpair_instance ( )
staticprivate

Create an instance of the SmoothEnvPairPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_SmoothEnvPairPotential().

SplitUnfoldedTwoBodyPotentialOP core::scoring::ScoringManager::create_split_unfolded_2body_potential_instance ( std::string const &  label_type,
std::string const &  value_type,
std::string const &  score_func_type 
)
staticprivate
utility::libsvm::Svm_rosettaOP core::scoring::ScoringManager::create_svm_rosetta ( std::string const &  filename)
staticprivate

Create an instance of an SVM, reading data from disk.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::scoring::TR().

Referenced by get_nmer_svm().

rna::TNA_SuitePotentialOP core::scoring::ScoringManager::create_tna_suitepotential_instance ( )
staticprivate

Create an instance of the TNA_SuitePotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Andy Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

Referenced by get_tna_suite_potential().

UnfoldedStatePotentialOP core::scoring::ScoringManager::create_unfolded_state_potential_instance ( std::string const &  type)
staticprivate

Create an instance of the UnfoldedStatePotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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().

VdWTinkerPotentialOP core::scoring::ScoringManager::create_vdw_tinker_potential_instance ( )
staticprivate

Create an instance of the VdWTinkerPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by get_VdWTinkerPotential().

WaterAdductHBondPotentialOP core::scoring::ScoringManager::create_water_adduct_hbond_potential_instance ( )
staticprivate

Create an instance of the WaterAdductHBondPotential object, by owning pointer.

Needed for threadsafe creation. Loads data from disk. NOT for repeated calls!

Note
Not intended for use outside of ScoringManager.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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.

Author
Hahnbeom Park (new logic for etable)
Note
One weak point of this method is that, change in frequently called but less relevant options such as weights, will invoke another etable construction.

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.

Author
Thread-safety added by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
Each element in the atom_vdw_ map is now threadsafe and lazily loaded (independently). Each of these objects is also threadsafe, as far as I can tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

Note
Each element in the atom_vdw_ map is now threadsafe and lazily loaded (independently).
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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).

Note
The lazy loading has been made threadsafe, as of the wee hours of 26 July 2017.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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).

Note
The lazy loading has been made threadsafe.
Author
Chris Bailey-Kellogg (cbk@c.nosp@m.s.da.nosp@m.rtmou.nosp@m.th.e.nosp@m.du), copied from Vikram K. Mulligan's netcharge_energy

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).

Note
The lazy loading has been made threadsafe.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

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

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.

Note
Whatever atom type set name and min occ energy are passed to this function the FIRST time determine the object that gets created. These parameters are unused in subsequent invocations. This aside, the targeted object is threadsafe, as far as I can tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

Note
Whatever atom type set name and min occ energy are passed to this function the FIRST time determine the object that gets created. These parameters are unused in subsequent invocations.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan.

Threadsafe and lazily loaded.

Author
Rewritten by Vikram K. Mulligan.

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
The FACTSPotential caches pose data to the global FACTSPotential object during scoring. As such, it is fundamentally NOT THREADSAFE!!! (Only the creation of this object is threadsafe).
Author
Rewritten by Vikram K. Mulligan.

Threadsafe and lazily loaded.

Author
Rewritten by Vikram K. Mulligan.

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan.

Threadsafe and lazily loaded.

Author
Rewritten by Vikram K. Mulligan.

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan.

Threadsafe and lazily loaded.

Author
Rewritten by Vikram K. Mulligan.

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
The Membrane_FAPotential object is fundamentally NOT THREADSAFE!!!
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

This is a PreLoaded csv containing, for example, NetMHCII data to be used by MHCEpitopePredictorPreLoaded.

Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

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.

Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

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.

Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
The MultipoleElecPotential caches pose data to the global MultipleElecPotential object during scoring. As such, it is fundamentally NOT THREADSAFE!!! (Only the creation of this object is threadsafe.)
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Author
Brahm Yachnin (brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du).

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.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
imv@u.nosp@m.w.ed.nosp@m.u
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded. Used by AbegoEnergy.

Author
imv@u.nosp@m.w.ed.nosp@m.u
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan.

Threadsafe and lazily loaded.

Author
Rewritten by Vikram K. Mulligan.PairEPotential const &

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Each restype stores separate tables for general and pre-proline scoring. The prepro_table parameter determines whether we're loading the default scoring table or the version for residues occurring before a proline.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
The Ramachandran object does lazily load custom cumulative distribution functions. However, these are finite and governed by an enum. In the MULTI_THREADED case, these are all loaded on object creation, which should get around thread- safety issues.
Author
Rewritten by Vikram K. Mulligan.

Threadsafe and lazily loaded.

Author
Rewritten by Vikram K. Mulligan.

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
The Ramachandran object does lazily load custom cumulative distribution functions. However, these are finite and governed by an enum. In the MULTI_THREADED case, these are all loaded on object creation, which should get around thread- safety issues.
Author
Rewritten by Vikram K. Mulligan.

Threadsafe and lazily loaded.

Author
Rewritten by Vikram K. Mulligan.

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
The RNA_DMS_LowResolutionPotential itself is fundamentally NOT THREADSAFE!!! Note that this function returns a non-const instance (which it shouldn't).
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

Note
The RNA_DMS_LowResolutionPotential itself is fundamentally NOT THREADSAFE!!!
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
The RNA_DMS_Potential itself is fundamentally NOT THREADSAFE!!! Note that this function returns a non-const instance (which it shouldn't).
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

Note
The RNA_DMS_Potential itself is fundamentally NOT THREADSAFE!!!
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Andrew Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

Threadsafe and lazily loaded.

Author
Rewritten by Andrew Watkins using templates by Vikram Mulligan

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).rna::RNP_LowResStackData const &

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
The RNA_SuitePotential caches pose-specific scoring data in the global instance of the TNA_SuitePotential object. As such, it is fundamentally NOT THREADSAFE. (but this can and will be easily corrected)
Author
Andy Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u).

Threadsafe and lazily loaded.

Author
Andy Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

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.

Note
Targeted object is also threadsafe, to the best of my ability to tell.
Author
Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Threadsafe and lazily loaded.

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

References create_water_adduct_hbond_potential_instance(), and water_adduct_hbond_potential_.

bool core::scoring::ScoringManager::has_energy_method ( ScoreType  score_type) const

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.

Note
This is threadsafe but ugly – it creates a new object every time it's invoked.

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.

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

References create_memb_etable_instance(), and memb_etables_.

Friends And Related Function Documentation

friend class utility::SingletonBase< ScoringManager >
friend

Member Data Documentation

std::map< std::string, core::scoring::aa_composition_energy::AACompositionEnergySetupOP > core::scoring::ScoringManager::aa_composition_setup_helpers_
mutableprivate

Cached data used by the AACompositionEnergy.

Accessor function has been made threadsafe (as of the wee hours of 26 July 2017).

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

Referenced by get_cloned_aa_comp_setup_helpers().

std::map< std::string, AtomVDWOP > core::scoring::ScoringManager::atom_vdw_
mutableprivate

Referenced by get_AtomVDW().

carbohydrates::OmegaPreferencesFunctionOP core::scoring::ScoringManager::carbohydrate_omega_preferences_function_
mutableprivate
carbon_hbonds::CarbonHBondPotentialOP core::scoring::ScoringManager::carbon_hbond_potential_
mutableprivate
disulfides::CentroidDisulfidePotentialOP core::scoring::ScoringManager::cen_disulfide_potential_
mutableprivate
CenHBPotentialOP core::scoring::ScoringManager::cen_hb_potential_
mutableprivate

Referenced by get_CenHBPotential().

CenRotEnvPairPotentialOP core::scoring::ScoringManager::cen_rot_pair_potential_
mutableprivate
carbohydrates::CHIEnergyFunctionOP core::scoring::ScoringManager::CHI_energy_function_
mutableprivate

Referenced by get_CHIEnergyFunction().

core::scoring::elec::CPRepMapTypeOP core::scoring::ScoringManager::cp_rep_map_byname_
mutableprivate

Cached data used by FA_ElecEnergy with beta_nov15.

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

Referenced by get_cp_rep_map_byname().

interface_::DDPlookupOP core::scoring::ScoringManager::DDP_lookup_table_
mutableprivate

Referenced by get_DDPLookupTable().

disulfides::DisulfideMatchingPotentialOP core::scoring::ScoringManager::disulfide_matching_potential_
mutableprivate
dna::DNA_BasePotentialOP core::scoring::ScoringManager::DNA_base_potential_
mutableprivate

Referenced by get_DNA_BasePotential().

dna::DNA_DihedralPotentialOP core::scoring::ScoringManager::dna_dihedral_potential_
mutableprivate
dna::DirectReadoutPotentialOP core::scoring::ScoringManager::dna_dr_potential_
mutableprivate
dna::DNA_EnvPairPotentialOP core::scoring::ScoringManager::dna_env_pair_potential_
mutableprivate
dna::DNATorsionPotentialOP core::scoring::ScoringManager::dna_torsion_potential_
mutableprivate

Referenced by get_DNATorsionPotential().

dna::DNABFormPotentialOP core::scoring::ScoringManager::dnabform_
mutableprivate

Referenced by get_DNABFormPotential().

EnvPairPotentialOP core::scoring::ScoringManager::env_pair_potential_
mutableprivate

Referenced by get_EnvPairPotential().

std::map< etable::EtableOptions, etable::EtableOP > core::scoring::ScoringManager::etables_by_options_
mutableprivate

Referenced by etable().

disulfides::FullatomDisulfidePotentialOP core::scoring::ScoringManager::fa_disulfide_potential_
mutableprivate
FACTSPotentialOP core::scoring::ScoringManager::facts_potential_
mutableprivate

Referenced by get_FACTSPotential().

GenBornPotentialOP core::scoring::ScoringManager::gen_born_potential_
mutableprivate

Referenced by get_GenBornPotential().

GenericBondedPotentialOP core::scoring::ScoringManager::generic_bonded_potential_
mutableprivate
HydroxylTorsionPotentialOP core::scoring::ScoringManager::hxl_tors_potential_
mutableprivate
std::map< std::string, loop_graph::evaluator::SixDTransRotPotentialOP > core::scoring::ScoringManager::loop_close_six_d_potential_
mutableprivate
std::map< std::string, etable::MembEtableOP > core::scoring::ScoringManager::memb_etables_
mutableprivate

Referenced by add_memb_etable(), and memb_etable().

Membrane_FAPotentialOP core::scoring::ScoringManager::membrane_fapotential_
mutableprivate
MembranePotentialOP core::scoring::ScoringManager::membrane_potential_
mutableprivate

Referenced by get_MembranePotential().

utility::vector1< methods::EnergyMethodCreatorOP > core::scoring::ScoringManager::method_creator_map_
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().

std::map< std::string, utility::pointer::shared_ptr< std::list< std::string > > > core::scoring::ScoringManager::mhc_csv_db_contents_map_
mutableprivate

Referenced by get_mhc_csv_contents().

std::map< std::string, core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP > core::scoring::ScoringManager::mhc_epitope_setup_helpers_
mutableprivate

Cached data used by the MHCEpitopeEnergy.

Accessor function has been made threadsafe.

Author
Chris Bailey-Kellogg (cbk@c.nosp@m.s.da.nosp@m.rtmou.nosp@m.th.e.nosp@m.du), copied from Vikram K. Mulligan's netcharge_energy

Referenced by get_cloned_mhc_epitope_setup_helpers().

std::map< std::string, utility::pointer::shared_ptr< std::list< std::string > > > core::scoring::ScoringManager::mhc_matrix_contents_map_
mutableprivate

Referenced by get_mhc_matrix_contents().

std::map< std::string, utility::pointer::shared_ptr< std::pair<std::map<std::string, core::Real>, core::Size> > > core::scoring::ScoringManager::mhc_sqlite_db_contents_map_
mutableprivate

Referenced by get_mhc_map_from_db().

mm::MMBondAngleLibraryOP core::scoring::ScoringManager::mm_bondangle_library_
mutableprivate

Referenced by get_MMBondAngleLibrary().

mm::MMBondLengthLibraryOP core::scoring::ScoringManager::mm_bondlength_library_
mutableprivate

Referenced by get_MMBondLengthLibrary().

mm::MMLJEnergyTableOP core::scoring::ScoringManager::mm_lj_energy_table_
mutableprivate

Referenced by get_MMLJEnergyTable().

mm::MMLJLibraryOP core::scoring::ScoringManager::mm_lj_library_
mutableprivate

Referenced by get_MMLJLibrary().

mm::MMTorsionLibraryOP core::scoring::ScoringManager::mm_torsion_library_
mutableprivate

Referenced by get_MMTorsionLibrary().

membrane::MembraneDataOP core::scoring::ScoringManager::mp_base_potential_
mutableprivate

Referenced by get_MembraneData().

MultipoleElecPotentialOP core::scoring::ScoringManager::multipole_elec_potential_
mutableprivate
std::map< std::string, core::scoring::netcharge_energy::NetChargeEnergySetupOP > core::scoring::ScoringManager::netcharge_setup_helpers_
mutableprivate

Cached data used by the NetChargeEnergy.

Accessor function has been made threadsafe.

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

Referenced by get_cloned_netcharge_setup_helpers().

std::map< std::string, utility::pointer::shared_ptr< std::map<core::chemical::AA, utility::vector1<core::Real> > > > core::scoring::ScoringManager::nmer_pssm_map_
mutableprivate

Referenced by get_nmer_pssm().

std::map< std::string, utility::pointer::shared_ptr< std::map< char, utility::vector1< core::Real > > > > core::scoring::ScoringManager::nmer_svm_aa_matrix_map_
mutableprivate

Referenced by get_nmer_svm_aa_matrix().

std::map< std::string, utility::pointer::shared_ptr< std::string > > core::scoring::ScoringManager::nmer_svm_list_file_contents_map_
mutableprivate
std::map< std::string, utility::libsvm::Svm_rosettaOP > core::scoring::ScoringManager::nmer_svm_map_
mutableprivate

Referenced by get_nmer_svm().

std::map< std::string, utility::pointer::shared_ptr< std::string > > core::scoring::ScoringManager::nmer_svm_rank_list_file_contents_map_
mutableprivate
std::map< std::string, utility::pointer::shared_ptr< utility::vector1< core::Real > > > core::scoring::ScoringManager::nmer_svm_rank_map_
mutableprivate

Referenced by get_nmer_svm_rank().

nv::NVlookupOP core::scoring::ScoringManager::NV_lookup_table_
mutableprivate

Referenced by get_NVLookupTable().

geometric_solvation::DatabaseOccSolEneOP core::scoring::ScoringManager::occ_hbond_sol_database_
mutableprivate

Referenced by get_DatabaseOccSolEne().

OmegaTetherOP core::scoring::ScoringManager::omega_
mutableprivate

Referenced by get_OmegaTether().

orbitals::OrbitalsLookupOP core::scoring::ScoringManager::orbitals_lookup_table_
mutableprivate

Referenced by get_OrbitalsLookupTable().

P_AAOP core::scoring::ScoringManager::p_aa_
mutableprivate

Referenced by get_P_AA().

P_AA_ssOP core::scoring::ScoringManager::p_aa_ss_
mutableprivate

Referenced by get_P_AA_ss().

P_AA_ABEGO3_OP core::scoring::ScoringManager::paa_abego3_
mutableprivate

Referenced by get_P_AA_ABEGO3().

PairEPotentialOP core::scoring::ScoringManager::pairE_potential_
mutableprivate

Referenced by get_PairEPotential().

PoissonBoltzmannPotentialOP core::scoring::ScoringManager::PB_potential_
mutableprivate
ProQPotentialOP core::scoring::ScoringManager::ProQ_potential_
mutableprivate

Referenced by get_ProQPotential().

PointWaterPotentialOP core::scoring::ScoringManager::pwp_
mutableprivate

Referenced by get_PointWaterPotential().

Ramachandran2BOP core::scoring::ScoringManager::rama2b_
mutableprivate

Referenced by get_Ramachandran2B_ptr().

RamachandranOP core::scoring::ScoringManager::rama_
mutableprivate

Referenced by get_Ramachandran_ptr().

RamaPreProOP core::scoring::ScoringManager::rama_pp_
mutableprivate

Referenced by get_RamaPrePro().

std::map< std::string, core::chemical::mainchain_potential::MainchainScoreTableOP > core::scoring::ScoringManager::rama_prepro_mainchain_potentials_
mutableprivate

Cached mainchain torsion potentials, used by rama_prepro.

This one is for potentials for residues NOT occurring before proline.

Note
The lazy-loading accessor function has been made threadsafe.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by get_rama_prepro_mainchain_torsion_potential().

std::map< std::string, core::chemical::mainchain_potential::MainchainScoreTableOP > core::scoring::ScoringManager::rama_prepro_mainchain_potentials_beforeproline_
mutableprivate

Cached mainchain torsion potentials, used by rama_prepro.

This one is for potentials for residues occurring before proline.

Note
The lazy-loading accessor function has been made threadsafe.
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by get_rama_prepro_mainchain_torsion_potential().

rna::RNA_AtomVDWOP core::scoring::ScoringManager::rna_atom_vdw_
mutableprivate

Referenced by get_RNA_AtomVDW().

rna::chemical_shift::RNA_ChemicalShiftPotentialOP core::scoring::ScoringManager::rna_chemical_shift_potential_
mutableprivate
rna::data::RNA_DMS_LowResolutionPotentialOP core::scoring::ScoringManager::rna_dms_low_resolution_potential_
mutableprivate
rna::data::RNA_DMS_PotentialOP core::scoring::ScoringManager::rna_dms_potential_
mutableprivate

Referenced by get_RNA_DMS_Potential().

std::map< std::string, rna::RNA_LowResolutionPotentialOP > core::scoring::ScoringManager::rna_low_resolution_potential_
mutableprivate
std::map< std::pair< bool, std::string >, rna::RNA_SuitePotentialOP > core::scoring::ScoringManager::rna_suite_potential_
mutableprivate

Referenced by get_rna_suite_potential().

rna::RNP_LowResPairDistPotentialOP core::scoring::ScoringManager::rnp_low_res_pair_dist_potential_
mutableprivate
rna::RNP_LowResPotentialOP core::scoring::ScoringManager::rnp_low_res_potential_
mutableprivate

Referenced by get_RNP_LowResPotential().

rna::RNP_LowResStackDataOP core::scoring::ScoringManager::rnp_low_res_stack_data_
mutableprivate

Referenced by get_RNP_LowResStackData().

SASAPotentialOP core::scoring::ScoringManager::sasa_potential_
mutableprivate

Referenced by get_SASAPotential().

SecondaryStructurePotentialOP core::scoring::ScoringManager::secondary_structure_potential_
mutableprivate
SmoothEnvPairPotentialOP core::scoring::ScoringManager::smooth_env_pair_potential_
mutableprivate
SplitUnfoldedTwoBodyPotentialOP core::scoring::ScoringManager::sutbp_
mutableprivate
rna::TNA_SuitePotentialOP core::scoring::ScoringManager::tna_suite_potential_
mutableprivate

Referenced by get_tna_suite_potential().

UnfoldedStatePotentialOP core::scoring::ScoringManager::unf_state_
mutableprivate
VdWTinkerPotentialOP core::scoring::ScoringManager::vdw_tinker_potential_
mutableprivate

Referenced by get_VdWTinkerPotential().

WaterAdductHBondPotentialOP core::scoring::ScoringManager::water_adduct_hbond_potential_
mutableprivate

The documentation for this class was generated from the following files: