Rosetta 3.4
|
#include <OccludedHbondSolEnergy_onebody.hh>
Public Member Functions | |
OccludedHbondSolEnergy_onebody (methods::EnergyMethodOptions const &options, bool const verbose=false) | |
OccludedHbondSolEnergy_onebody (OccludedHbondSolEnergy_onebody const &src) | |
virtual methods::EnergyMethodOP | clone () const |
virtual void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const |
virtual void | setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > 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 | setup_for_minimizing (pose::Pose &pose, ScoreFunction const &, kinematics::MinimizerMapBase const &) const |
Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. | |
virtual void | residue_energy (conformation::Residue const &polar_rsd, pose::Pose const &pose, EnergyMap &emap) const |
Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them). | |
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. | |
virtual bool | defines_intrares_energy (EnergyMap const &) const |
virtual Distance | atomic_interaction_cutoff () const |
Public Attributes | |
__pad0__:ContextDependentOneBodyEnergy parent |
core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::OccludedHbondSolEnergy_onebody | ( | methods::EnergyMethodOptions const & | options, |
bool const | verbose = false |
||
) |
References core::scoring::geometric_solvation::tr().
Referenced by clone().
core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::OccludedHbondSolEnergy_onebody | ( | OccludedHbondSolEnergy_onebody const & | src | ) |
References core::scoring::geometric_solvation::tr().
Distance core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atomic_interaction_cutoff | ( | ) | const [virtual] |
methods::EnergyMethodOP core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::clone | ( | ) | const [virtual] |
Implements core::scoring::methods::EnergyMethod.
References OccludedHbondSolEnergy_onebody().
virtual bool core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::defines_intrares_energy | ( | EnergyMap const & | ) | const [inline, virtual] |
virtual void core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::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.
void core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy | ( | conformation::Residue const & | rsd, |
pose::Pose const & | pose, | ||
EnergyMap & | emap | ||
) | const [virtual] |
Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them).
Implements core::scoring::methods::ContextDependentOneBodyEnergy.
References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::graph::Node::const_edge_list_begin(), core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::graph::Graph::get_node(), core::conformation::Residue::Hpos_polar(), core::conformation::Residue::natoms(), core::scoring::occ_sol_fitted_onebody, core::pose::Pose::residue(), core::conformation::Residue::seqpos(), and core::scoring::Energies::tenA_neighbor_graph().
void core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::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::geometric_solvation::tr().
void core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::setup_for_minimizing | ( | pose::Pose & | , |
ScoreFunction const & | , | ||
kinematics::MinimizerMapBase const & | |||
) | const [virtual] |
Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true.
default implementation noop
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::geometric_solvation::tr().
void core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::setup_for_packing | ( | pose::Pose & | , |
utility::vector1< bool > const & | , | ||
utility::vector1< bool > const & | |||
) | const [virtual] |
default implementation noop
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_residue_neighbors().
void core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::setup_for_scoring | ( | pose::Pose & | pose, |
ScoreFunction const & | |||
) | const [virtual] |
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_residue_neighbors().