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Rosetta 3.4
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Rosetta 3.4
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#include <ElecDensAllAtomCenEnergy.hh>
Public Member Functions | |
| ElecDensAllAtomCenEnergy () | |
| c-tor | |
| virtual methods::EnergyMethodOP | clone () const |
| clone | |
| methods::LongRangeEnergyType | long_range_type () const |
| virtual bool | defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const |
| virtual void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sf) const |
| Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. | |
| virtual bool | defines_intrares_energy (EnergyMap const &) const |
| Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not. | |
| virtual void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the intra-residue constraint energy for a given residue. | |
| virtual void | residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. | |
| virtual void | finalize_total_energy (pose::Pose const &pose, ScoreFunction const &, EnergyMap &totals) const |
| called at the end of energy evaluation | |
| virtual void | eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const |
| called during gradient-based minimization inside dfunc | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. | |
Public Attributes | |
| __pad0__:ContextDependentLRTwoBodyEnergy parent | |
| core::scoring::electron_density::ElecDensAllAtomCenEnergy::ElecDensAllAtomCenEnergy | ( | ) |
c-tor
References core::scoring::electron_density::getDensityMap(), and core::scoring::electron_density::ElectronDensity::isMapLoaded().
Referenced by clone().
| methods::EnergyMethodOP core::scoring::electron_density::ElecDensAllAtomCenEnergy::clone | ( | ) | const [virtual] |
| virtual bool core::scoring::electron_density::ElecDensAllAtomCenEnergy::defines_intrares_energy | ( | EnergyMap const & | weights | ) | const [inline, virtual] |
Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.
For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.
Implements core::scoring::methods::TwoBodyEnergy.
| bool core::scoring::electron_density::ElecDensAllAtomCenEnergy::defines_residue_pair_energy | ( | pose::Pose const & | pose, |
| Size | res1, | ||
| Size | res2 | ||
| ) | const [virtual] |
| void core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative | ( | id::AtomID const & | id, |
| pose::Pose const & | pose, | ||
| kinematics::DomainMap const & | , | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap const & | weights, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const [virtual] |
called during gradient-based minimization inside dfunc
Reimplemented from core::scoring::methods::EnergyMethod.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::pose::Pose::conformation(), core::scoring::electron_density::ElectronDensity::dCCdx_aacen(), core::scoring::elec_dens_whole_structure_allatom, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_outgoing_edges(), core::scoring::electron_density::ElectronDensity::get_R(), core::kinematics::FoldTree::get_residue_edge(), core::scoring::electron_density::ElectronDensity::get_symmMap(), core::scoring::electron_density::getDensityMap(), core::pose::Pose::is_fullatom(), core::chemical::AtomType::is_heavyatom(), core::kinematics::FoldTree::is_root(), core::pose::symmetry::is_symmetric(), core::kinematics::FoldTree::jump_edge(), core::kinematics::Edge::label(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::scoring::electron_density::SQ(), core::scoring::rna::X, core::conformation::Atom::xyz(), and core::pose::Pose::xyz().
| void core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_intrares_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
Evaluate the intra-residue constraint energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
| void core::scoring::electron_density::ElecDensAllAtomCenEnergy::finalize_total_energy | ( | pose::Pose const & | pose, |
| ScoreFunction const & | , | ||
| EnergyMap & | totals | ||
| ) | const [virtual] |
called at the end of energy evaluation
| virtual void core::scoring::electron_density::ElecDensAllAtomCenEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [inline, virtual] |
Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
| methods::LongRangeEnergyType core::scoring::electron_density::ElecDensAllAtomCenEnergy::long_range_type | ( | ) | const [virtual] |
Implements core::scoring::methods::LongRangeTwoBodyEnergy.
References core::scoring::methods::elec_dens_allatom_cen_energy.
Referenced by setup_for_scoring().
| void core::scoring::electron_density::ElecDensAllAtomCenEnergy::residue_pair_energy | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
Implements core::scoring::methods::TwoBodyEnergy.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, and core::scoring::elec_dens_whole_structure_allatom.
| void core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives | ( | pose::Pose & | pose, |
| ScoreFunction const & | sfxn | ||
| ) | const [virtual] |
Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
default implementation noop
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::conformation(), core::scoring::electron_density::getDensityMap(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), and core::scoring::electron_density::ElectronDensity::matchPose().
| void core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| ScoreFunction const & | |||
| ) | const [virtual] |
Reimplemented from core::scoring::methods::EnergyMethod.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::kinematics::FoldTree::begin(), core::pose::Pose::conformation(), core::scoring::elec_dens_whole_structure_allatom, core::pose::Pose::energies(), core::pose::Pose::fold_tree(), core::scoring::electron_density::getDensityMap(), core::pose::symmetry::is_symmetric(), long_range_type(), core::scoring::electron_density::ElectronDensity::matchPose(), core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::set_nres(), core::kinematics::Edge::start(), core::pose::Pose::total_residue(), and core::scoring::electron_density::TR().
1.7.4
