Rosetta 3.4
Public Member Functions | Public Attributes
core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy Class Reference

#include <ExactOccludedHbondSolEnergy.hh>

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List of all members.

Public Member Functions

 ExactOccludedHbondSolEnergy (bool const exact_occ_skip_Hbonders=false, bool const exact_occ_include_Hbond_contribution=false, bool const exact_occ_pairwise=false, bool const exact_occ_pairwise_by_res=false, bool const exact_occ_split_between_res=false, bool const exact_occ_self_res_occ=true, core::Real const occ_radius_scaling=1., bool const verbose=false)
 ExactOccludedHbondSolEnergy (ExactOccludedHbondSolEnergy const &src)
 ~ExactOccludedHbondSolEnergy ()
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
core::Real compute_grid_constant (hbonds::HBEvalTuple const &hbond_eval_type) const
core::Real compute_polar_group_sol_energy (pose::Pose const &pose, conformation::Residue const &polar_rsd, Size const polar_atom, bool const restrict_to_single_occluding_residue=false, Size const single_occluding_resinx=0, bool const restrict_to_single_occluding_atom=false, Size const single_occluding_atominx=0) const
core::Real compute_polar_group_sol_energy (pose::Pose const &pose, conformation::Residue const &polar_rsd, core::Size const polar_atomno, GridInfo const &grid_info, core::Real const &grid_constant, std::vector< std::vector< std::vector< core::Real > > > const &water_weights, bool const restrict_to_single_occluding_residue=false, core::Size const single_occluding_resinx=0, bool const restrict_to_single_occluding_atom=false, core::Size const single_occluding_atominx=0) const

Public Attributes

 __pad0__:ContextDependentOneBodyEnergy parent

Constructor & Destructor Documentation

core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy ( bool const  exact_occ_skip_Hbonders = false,
bool const  exact_occ_include_Hbond_contribution = false,
bool const  exact_occ_pairwise = false,
bool const  exact_occ_pairwise_by_res = false,
bool const  exact_occ_split_between_res = false,
bool const  exact_occ_self_res_occ = true,
core::Real const  occ_radius_scaling = 1.,
bool const  verbose = false 
)
core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy ( ExactOccludedHbondSolEnergy const &  src)
core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::~ExactOccludedHbondSolEnergy ( )

Member Function Documentation

Distance core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::atomic_interaction_cutoff ( ) const [virtual]
methods::EnergyMethodOP core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::clone ( ) const [virtual]
core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_grid_constant ( hbonds::HBEvalTuple const &  hbond_eval_type) const
Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy ( pose::Pose const &  pose,
conformation::Residue const &  polar_rsd,
Size const  polar_atom,
bool const  restrict_to_single_occluding_residue = false,
Size const  single_occluding_resinx = 0,
bool const  restrict_to_single_occluding_atom = false,
Size const  single_occluding_atominx = 0 
) const
core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy ( pose::Pose const &  pose,
conformation::Residue const &  polar_rsd,
core::Size const  polar_atomno,
GridInfo const &  grid_info,
core::Real const &  grid_constant,
std::vector< std::vector< std::vector< core::Real > > > const &  water_weights,
bool const  restrict_to_single_occluding_residue = false,
core::Size const  single_occluding_resinx = 0,
bool const  restrict_to_single_occluding_atom = false,
core::Size const  single_occluding_atominx = 0 
) const

References core::conformation::Residue::abase2(), core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::graph::Node::const_edge_list_begin(), core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::geometric_solvation::geosol_kT, core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::hbonds::get_hbond_weight_type(), core::graph::Graph::get_node(), core::scoring::hbonds::get_seq_sep(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbacc_AHX, core::scoring::hbonds::hbacc_CXA, core::scoring::hbonds::hbacc_CXL, core::scoring::hbonds::hbacc_HXL, core::scoring::hbonds::hbacc_IMD, core::scoring::hbonds::hbacc_IME, core::scoring::hbonds::hbacc_PBA, core::scoring::hbonds::hbdon_AHX, core::scoring::hbonds::hbdon_AMO, core::scoring::hbonds::hbdon_CXA, core::scoring::hbonds::hbdon_GDE, core::scoring::hbonds::hbdon_GDH, core::scoring::hbonds::hbdon_HXL, core::scoring::hbonds::hbdon_IMD, core::scoring::hbonds::hbdon_IME, core::scoring::hbonds::hbdon_IND, core::scoring::hbonds::hbdon_PBA, core::scoring::hbonds::hbw_LR_BB, core::scoring::hbonds::hbw_SC, core::scoring::hbonds::hbw_SR_BB, core::conformation::Residue::Hpos_polar(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::scoring::geometric_solvation::SKIP_HBONDER_CUT, core::scoring::Energies::tenA_neighbor_graph(), core::scoring::geometric_solvation::GridInfo::xnum_points(), core::scoring::geometric_solvation::GridInfo::xorigin(), core::scoring::geometric_solvation::GridInfo::xstep(), protocols::kinmatch::xyz(), core::conformation::Atom::xyz(), core::scoring::geometric_solvation::GridInfo::ynum_points(), core::scoring::geometric_solvation::GridInfo::yorigin(), core::scoring::geometric_solvation::GridInfo::ystep(), core::scoring::geometric_solvation::GridInfo::znum_points(), core::scoring::geometric_solvation::GridInfo::zorigin(), and core::scoring::geometric_solvation::GridInfo::zstep().

virtual bool core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::defines_intrares_energy ( EnergyMap const &  ) const [inline, virtual]
virtual void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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::ExactOccludedHbondSolEnergy::residue_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap emap 
) const [virtual]
void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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::TR().

void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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::TR().

void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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::ExactOccludedHbondSolEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]

Member Data Documentation


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