Rosetta 3.4
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NatbiasSecondaryStructureEnergy. More...
#include <NatbiasSecondaryStructureEnergy.hh>
typedef core::Distance protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::Distance |
typedef core::scoring::EnergyMap protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::EnergyMap |
typedef core::scoring::methods::EnergyMethodOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::EnergyMethodOP |
typedef protocols::fldsgn::topology::HelixPairingSetOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::HelixPairingSetOP |
typedef protocols::fldsgn::topology::HSSTripletSetOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::HSSTripletSetOP |
typedef protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasHelicesSheetPotentialOP |
typedef protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasHelixPairPotentialOP |
typedef protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasStrandPairPotentialOP |
typedef core::scoring::methods::WholeStructureEnergy protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::parent |
Reimplemented from core::scoring::methods::WholeStructureEnergy.
typedef core::pose::Pose protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::Pose |
typedef core::scoring::ScoreFunction protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::ScoreFunction |
typedef protocols::fldsgn::topology::StrandPairingSetOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::StrandPairingSetOP |
typedef std::string protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::String |
protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasSecondaryStructureEnergy | ( | ) |
default constructor
Referenced by clone().
protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasSecondaryStructureEnergy | ( | NatbiasSecondaryStructureEnergy const & | src | ) |
copy constructor
core::Distance protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::atomic_interaction_cutoff | ( | ) | const [virtual] |
The NatbiasSecondaryStructureEnergy class requires that the EnergyGraph span 12 Angstroms between centroids. The centroids residues build-in a 3 Angstrom radius each.
SecondaryStructureEnergy distance cutoff.
Reimplemented from core::scoring::methods::WholeStructureEnergy.
NatbiasSecondaryStructureEnergy::EnergyMethodOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::clone | ( | ) | const [virtual] |
clone
Implements core::scoring::methods::EnergyMethod.
References NatbiasSecondaryStructureEnergy().
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::finalize_total_energy | ( | Pose & | pose, |
ScoreFunction const & | , | ||
EnergyMap & | totals | ||
) | const [virtual] |
scoring
all scoring happens here
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::natbias_hh, core::scoring::natbias_hs, core::scoring::natbias_ss, and core::pose::Pose::total_residue().
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [virtual] |
SecondaryStructureEnergy.
Implements core::scoring::methods::EnergyMethod.
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::native_secstruct | ( | String const & | secstruct | ) |
set native secondary structure
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot | ( | NatbiasHelicesSheetPotentialOP const | hspot | ) |
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot | ( | HSSTripletSetOP const | hss3set | ) |
set NatbiasHelicesSheetPotential
set HelicesSheetPotential
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot | ( | HelixPairingSetOP const | hpairset | ) |
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot | ( | NatbiasHelixPairPotentialOP const | hhpot | ) |
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot | ( | NatbiasStrandPairPotentialOP const | sspot | ) |
set native NatbiasStrandPairPotential
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot | ( | StrandPairingSetOP const | spairset | ) |
set NatbiasStrandPairPotential
set native NatbiasStrandPairPotential
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::setup_for_scoring | ( | Pose & | pose, |
ScoreFunction const & | scorefxn | ||
) | const [virtual] |
scoring
set up for scoring
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_residue_neighbors().
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias | ( | bool const | b | ) | [inline] |
use use original secondary structure potential
References protocols::match::upstream::b.
core::Size protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::version | ( | ) | const [virtual] |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.