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Rosetta 3.4
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Rosetta 3.4
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#include <ContextIndependentGeometricSolEnergy.hh>
Public Member Functions | |
| ContextIndependentGeometricSolEnergy (methods::EnergyMethodOptions const &options) | |
| copy c-tor | |
| ContextIndependentGeometricSolEnergy (ContextIndependentGeometricSolEnergy const &src) | |
| copy c-tor | |
| virtual methods::EnergyMethodOP | clone () const |
| clone | |
| virtual void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const |
| Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. | |
| virtual void | residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const |
| Everything in here. | |
| void | eval_atom_derivative_intra_RNA (id::AtomID const &atom_id, pose::Pose const &pose, EnergyMap const &weights, Vector &F1, Vector &F2) const |
| virtual void | eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const |
| f1 and f2 are zeroed | |
| Real | eval_atom_energy (id::AtomID const &atom_id, pose::Pose const &pose) const |
| virtual bool | defines_intrares_energy (EnergyMap const &weights) 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 &, EnergyMap &emap) const |
| Evaluate the intra-residue energy for a given residue. | |
| virtual Distance | atomic_interaction_cutoff () const |
| HACK! MAX_R defines the maximum donorH to acceptor distance. | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| ContextIndependentGeometricSolEnergy is NOT context sensitive. | |
Public Attributes | |
| __pad0__:ContextIndependentTwoBodyEnergy parent | |
| core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::ContextIndependentGeometricSolEnergy | ( | methods::EnergyMethodOptions const & | options | ) |
copy c-tor
Referenced by clone().
| core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::ContextIndependentGeometricSolEnergy | ( | ContextIndependentGeometricSolEnergy const & | src | ) |
copy c-tor
copy ctor
| Distance core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::atomic_interaction_cutoff | ( | ) | const [virtual] |
HACK! MAX_R defines the maximum donorH to acceptor distance.
Implements core::scoring::methods::ShortRangeTwoBodyEnergy.
References core::scoring::hbonds::MAX_R.
| methods::EnergyMethodOP core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::clone | ( | ) | const [virtual] |
clone
Implements core::scoring::methods::EnergyMethod.
References ContextIndependentGeometricSolEnergy().
| bool core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::defines_intrares_energy | ( | EnergyMap const & | weights | ) | const [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.
References core::scoring::CI_geom_sol_intra_RNA.
| void core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative | ( | id::AtomID const & | atom_id, |
| pose::Pose const & | pose, | ||
| kinematics::DomainMap const & | , | ||
| ScoreFunction const & | , | ||
| EnergyMap const & | weights, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const [virtual] |
f1 and f2 are zeroed
Reimplemented from core::scoring::methods::EnergyMethod.
References core::id::AtomID::atomno(), core::scoring::CI_geom_sol, core::scoring::hbonds::HBondDerivs::don_deriv, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), eval_atom_derivative_intra_RNA(), core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), core::scoring::hbonds::HBondDerivs::h_deriv, core::pose::Pose::residue(), and core::id::AtomID::rsd().
| void core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative_intra_RNA | ( | id::AtomID const & | atom_id, |
| pose::Pose const & | pose, | ||
| EnergyMap const & | weights, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const |
References core::id::AtomID::atomno(), core::scoring::CI_geom_sol_intra_RNA, core::scoring::hbonds::HBondDerivs::don_deriv, core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), core::scoring::hbonds::HBondDerivs::h_deriv, core::scoring::rna::Is_base_phosphate_atom_pair(), core::pose::Pose::residue(), and core::id::AtomID::rsd().
Referenced by eval_atom_derivative().
| Real core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_energy | ( | id::AtomID const & | atom_id, |
| pose::Pose const & | pose | ||
| ) | const |
| void core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_intrares_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
Evaluate the intra-residue energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
References core::scoring::CI_geom_sol_intra_RNA, and core::conformation::Residue::is_RNA().
| void core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | ) | const [virtual] |
ContextIndependentGeometricSolEnergy is NOT context sensitive.
Implements core::scoring::methods::EnergyMethod.
| void core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::residue_pair_energy | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | , | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
Everything in here.
This evaluates everything for now, but eventually may want to split this based on backbone/backbone vs. others, as is carried out in HBondEnergy.cc
Implements core::scoring::methods::TwoBodyEnergy.
References core::scoring::CI_geom_sol, core::conformation::Residue::is_RNA(), and core::conformation::Residue::seqpos().
| void core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::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::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::hbonds::fill_hbond_set(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().
| void core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| ScoreFunction const & | |||
| ) | const [virtual] |
1.7.4
