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core::scoring::geometric_solvation::GeometricSolEnergyEvaluator Class Reference

#include <GeometricSolEnergyEvaluator.hh>

Inheritance diagram for core::scoring::geometric_solvation::GeometricSolEnergyEvaluator:
Inheritance graph
[legend]

Public Member Functions

 GeometricSolEnergyEvaluator (methods::EnergyMethodOptions const &opts)
 copy c-tor More...
 
 GeometricSolEnergyEvaluator (GeometricSolEnergyEvaluator const &src)
 copy ctor More...
 
 ~GeometricSolEnergyEvaluator () override
 
void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 
Real eval_atom_energy (id::AtomID const &atom_id, pose::Pose const &pose) const
 
void eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 
Distance atomic_interaction_cutoff () const
 HACK! MAX_R defines the maximum donorH to acceptor distance. More...
 
Real geometric_sol_one_way_bb_bb (conformation::Residue const &polar_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
Real geometric_sol_one_way_sc (conformation::Residue const &polar_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
Real res_res_geometric_sol_one_way (conformation::Residue const &polar_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
bool atom_is_heavy (conformation::Residue const &rsd, Size const atm) const
 
void get_atom_atom_geometric_solvation_for_donor (Size const don_h_atm, conformation::Residue const &don_rsd, Size const occ_atm, conformation::Residue const &occ_rsd, pose::Pose const &pose, Real &energy, bool const update_deriv=false, hbonds::HBondDerivs &deriv=core::scoring::hbonds::DUMMY_DERIVS, hbonds::HBEvalTuple &hbe=core::scoring::hbonds::DUMMY_HBE) const
 
void get_atom_atom_geometric_solvation_for_acceptor (Size const acc_atm, conformation::Residue const &acc_rsd, Size const occ_atm, conformation::Residue const &occ_rsd, pose::Pose const &pose, Real &energy, bool const update_deriv=false, hbonds::HBondDerivs &deriv=core::scoring::hbonds::DUMMY_DERIVS, hbonds::HBEvalTuple &hbe=core::scoring::hbonds::DUMMY_HBE) const
 
void eval_intrares_derivatives (conformation::Residue const &rsd, pose::Pose const &pose, Real const &geom_sol_intra_weight, utility::vector1< DerivVectorPair > &atom_derivs, bool const just_rna=false) const
 
void eval_residue_pair_derivatives (conformation::Residue const &ires, conformation::Residue const &jres, ResPairMinimizationData const &min_data, pose::Pose const &pose, Real const geom_sol_weight, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
 
Real residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose) const
 
bool defines_score_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, bool res_moving_wrt_eachother) const
 
etable::count_pair::CountPairFunctionCOP get_count_pair_function (Size const res1, Size const res2, pose::Pose const &pose) const
 
etable::count_pair::CountPairFunctionCOP get_count_pair_function (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
 
etable::count_pair::CountPairFunctionCOP get_intrares_countpair (conformation::Residue const &res) const
 
void setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData &pair_data) const
 
Real precalculate_bb_bb_energy_for_design (pose::Pose const &pose) const
 

Private Member Functions

bool check_path_distance (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Size const &atm1, Size const &atm2) const
 
Real donorRes_occludingRes_geometric_sol_one_way (conformation::Residue const &don_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
Real acceptorRes_occludingRes_geometric_sol_one_way (conformation::Residue const &acc_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
Real donorRes_occludingRes_geometric_sol_one_way_bb_bb (conformation::Residue const &don_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
Real acceptorRes_occludingRes_geometric_sol_one_way_bb_bb (conformation::Residue const &acc_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
Real donorRes_occludingRes_geometric_sol_one_way_sc (conformation::Residue const &don_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
Real acceptorRes_occludingRes_geometric_sol_one_way_sc (conformation::Residue const &acc_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
 
Real occluded_water_hbond_penalty (bool const &is_donor, hbonds::HBEvalTuple const &hbond_eval_type, Vector const &polar_atm_xyz, Vector const &base_atm_xyz, Vector const &base2_atm_xyz, Vector const &occluding_atm_xyz, Size const &polar_nb, Size const &occ_nb, bool const update_deriv=false, hbonds::HBondDerivs &deriv=core::scoring::hbonds::DUMMY_DERIVS) const
 
void set_water_base_atm (Vector const &base_v, Vector const &atom_v, Vector const &water_v, Vector &water_base_v, Real const &xH, Distance const &bond_length) const
 
Real get_water_cos (Vector const &base_atm_xyz, Vector const &polar_atm_xyz, Vector const &occluding_atm_xyz) const
 Compute the cosine required for calling water Hbond energies. More...
 
Real donorRes_occludingRes_geometric_sol_intra (conformation::Residue const &rsd, pose::Pose const &pose, bool const just_RNA=false) const
 
Real acceptorRes_occludingRes_geometric_sol_intra (conformation::Residue const &rsd, pose::Pose const &pose, bool const just_RNA=false) const
 
Vector get_acceptor_base_atm_xyz (conformation::Residue const &acc_rsd, Size const &acc_atm, hbonds::HBEvalTuple const &hbt) const
 

Private Attributes

methods::EnergyMethodOptions
const & 
options_
 
hbonds::HBondDatabaseCOP hb_database_
 
Real const dist_cut2_
 
Real const geometric_sol_scale_
 
int const interres_path_distance_cutoff_
 
int const intrares_path_distance_cutoff_
 
int path_distance_
 
bool const verbose_
 

Constructor & Destructor Documentation

core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::GeometricSolEnergyEvaluator ( methods::EnergyMethodOptions const &  opts)

copy c-tor

core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::GeometricSolEnergyEvaluator ( GeometricSolEnergyEvaluator const &  src)

copy ctor

core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::~GeometricSolEnergyEvaluator ( )
overridedefault

Member Function Documentation

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
bool const  just_RNA = false 
) const
private
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way ( conformation::Residue const &  acc_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
inlineprivate
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb ( conformation::Residue const &  acc_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
inlineprivate
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc ( conformation::Residue const &  acc_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
inlineprivate
bool core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy ( conformation::Residue const &  rsd,
Size const  atm 
) const
Distance core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atomic_interaction_cutoff ( ) const

HACK! MAX_R defines the maximum donorH to acceptor distance.

References core::scoring::hbonds::MAX_R.

bool core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Size const &  atm1,
Size const &  atm2 
) const
private
bool core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::defines_score_for_residue_pair ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
bool  res_moving_wrt_eachother 
) const
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
bool const  just_RNA = false 
) const
private
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way ( conformation::Residue const &  don_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
inlineprivate
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb ( conformation::Residue const &  don_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
inlineprivate
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc ( conformation::Residue const &  don_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
inlineprivate
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy ( id::AtomID const &  atom_id,
pose::Pose const &  pose 
) const
void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
Real const &  geom_sol_intra_weight,
utility::vector1< DerivVectorPair > &  atom_derivs,
bool const  just_rna = false 
) const
void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  ,
EnergyMap emap 
) const
void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives ( conformation::Residue const &  ires,
conformation::Residue const &  jres,
ResPairMinimizationData const &  min_data,
pose::Pose const &  pose,
Real const  geom_sol_weight,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::geometric_sol_one_way_bb_bb ( conformation::Residue const &  polar_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::geometric_sol_one_way_sc ( conformation::Residue const &  polar_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
Vector core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz ( conformation::Residue const &  acc_rsd,
Size const &  acc_atm,
hbonds::HBEvalTuple const &  hbt 
) const
inlineprivate
void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor ( Size const  acc_atm,
conformation::Residue const &  acc_rsd,
Size const  occ_atm,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose,
Real energy,
bool const  update_deriv = false,
hbonds::HBondDerivs deriv = core::scoring::hbonds::DUMMY_DERIVS,
hbonds::HBEvalTuple hbe = core::scoring::hbonds::DUMMY_HBE 
) const

References core::conformation::Residue::abase2(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), check_path_distance(), core::scoring::Energies::data(), dist_cut2_, core::pose::Pose::energies(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::chemical::element::F, core::scoring::hbonds::get_hb_acc_chem_type(), core::conformation::Residue::has_variant_type(), core::scoring::hbonds::hbdon_H2O, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::conformation::Residue::heavyatom_has_polar_hydrogens(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::element::I, core::conformation::Residue::is_protein(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name1(), occluded_water_hbond_penalty(), options_, path_distance_, core::chemical::REPLONLY, core::scoring::hbonds::seq_sep_other, core::conformation::Residue::seqpos(), core::scoring::Energies::tenA_neighbor_graph(), core::scoring::TR(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), verbose_, core::chemical::VIRTUAL_RNA_RESIDUE, core::conformation::Atom::xyz(), core::conformation::Residue::xyz(), and core::scoring::hbonds::ZERO_DERIV2D.

Referenced by acceptorRes_occludingRes_geometric_sol_intra(), acceptorRes_occludingRes_geometric_sol_one_way(), acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), acceptorRes_occludingRes_geometric_sol_one_way_sc(), eval_atom_energy(), eval_intrares_derivatives(), eval_residue_pair_derivatives(), and residue_pair_energy_ext().

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor ( Size const  don_h_atm,
conformation::Residue const &  don_rsd,
Size const  occ_atm,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose,
Real energy,
bool const  update_deriv = false,
hbonds::HBondDerivs deriv = core::scoring::hbonds::DUMMY_DERIVS,
hbonds::HBEvalTuple hbe = core::scoring::hbonds::DUMMY_HBE 
) const

References core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_is_polar_hydrogen(), core::conformation::Residue::atom_name(), check_path_distance(), core::scoring::Energies::data(), dist_cut2_, core::pose::Pose::energies(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::chemical::element::F, core::conformation::Residue::has_variant_type(), core::scoring::hbonds::hbacc_HXL, core::scoring::hbonds::hbdon_HXL, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::element::I, core::conformation::Residue::is_protein(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name1(), occluded_water_hbond_penalty(), options_, path_distance_, core::chemical::REPLONLY, core::scoring::hbonds::seq_sep_other, core::conformation::Residue::seqpos(), core::scoring::Energies::tenA_neighbor_graph(), core::scoring::TR(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), verbose_, core::chemical::VIRTUAL_RNA_RESIDUE, core::conformation::Atom::xyz(), and core::scoring::hbonds::ZERO_DERIV2D.

Referenced by donorRes_occludingRes_geometric_sol_intra(), donorRes_occludingRes_geometric_sol_one_way(), donorRes_occludingRes_geometric_sol_one_way_bb_bb(), donorRes_occludingRes_geometric_sol_one_way_sc(), eval_atom_energy(), eval_intrares_derivatives(), eval_residue_pair_derivatives(), and residue_pair_energy_ext().

etable::count_pair::CountPairFunctionCOP core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function ( Size const  res1,
Size const  res2,
pose::Pose const &  pose 
) const
etable::count_pair::CountPairFunctionCOP core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
) const
etable::count_pair::CountPairFunctionCOP core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_intrares_countpair ( conformation::Residue const &  res) const
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_water_cos ( Vector const &  base_atm_xyz,
Vector const &  polar_atm_xyz,
Vector const &  occluding_atm_xyz 
) const
inlineprivate

Compute the cosine required for calling water Hbond energies.

Referenced by occluded_water_hbond_penalty().

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty ( bool const &  is_donor,
hbonds::HBEvalTuple const &  hbond_eval_type,
Vector const &  polar_atm_xyz,
Vector const &  base_atm_xyz,
Vector const &  base2_atm_xyz,
Vector const &  occluding_atm_xyz,
Size const &  polar_nb,
Size const &  occ_nb,
bool const  update_deriv = false,
hbonds::HBondDerivs deriv = core::scoring::hbonds::DUMMY_DERIVS 
) const
inlineprivate

References core::scoring::hbonds::HBondDerivs::abase2_deriv, core::scoring::hbonds::HBondDerivs::abase_deriv, core::scoring::hbonds::HBondDerivs::acc_deriv, core::scoring::hbonds::HBEvalTuple::acc_type(), core::scoring::hbonds::HBondDerivs::don_deriv, core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), geometric_sol_scale_, core::scoring::hbonds::get_environment_dependent_weight(), core::scoring::hbonds::get_hbe_acc_hybrid(), get_water_cos(), core::scoring::hbonds::HBondDerivs::h_deriv, hb_database_, core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbacc_AHX, core::scoring::hbonds::hbacc_HXL, core::scoring::hbonds::hbderiv_ABE_GO_GEOMSOL_OCC_ACC, core::scoring::hbonds::hbderiv_ABE_GO_GEOMSOL_OCC_DON, core::scoring::hbonds::hbond_compute_energy(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), core::scoring::hbonds::MAX_R2, core::scoring::hbonds::MAX_xD, core::scoring::hbonds::MAX_xH, core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy(), core::scoring::hbonds::MIN_R2, core::scoring::hbonds::MIN_xD, core::scoring::hbonds::MIN_xH, options_, set_water_base_atm(), core::chemical::SP2_HYBRID, core::scoring::TR(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty(), verbose_, and core::scoring::hbonds::ZERO_DERIV2D.

Referenced by get_atom_atom_geometric_solvation_for_acceptor(), and get_atom_atom_geometric_solvation_for_donor().

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::precalculate_bb_bb_energy_for_design ( pose::Pose const &  pose) const
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::res_res_geometric_sol_one_way ( conformation::Residue const &  polar_rsd,
conformation::Residue const &  occ_rsd,
pose::Pose const &  pose 
) const
void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  ,
EnergyMap emap 
) const
Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
ResPairMinimizationData const &  min_data,
pose::Pose const &  pose 
) const
void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::set_water_base_atm ( Vector const &  base_v,
Vector const &  atom_v,
Vector const &  water_v,
Vector water_base_v,
Real const &  xH,
Distance const &  bond_length 
) const
inlineprivate
void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::setup_for_minimizing_for_residue_pair ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
ResPairMinimizationData pair_data 
) const

Member Data Documentation

Real const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::dist_cut2_
private
Real const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::geometric_sol_scale_
private
hbonds::HBondDatabaseCOP core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::hb_database_
private
int const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::interres_path_distance_cutoff_
private

Referenced by check_path_distance().

int const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::intrares_path_distance_cutoff_
private

Referenced by check_path_distance().

methods::EnergyMethodOptions const& core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::options_
private
int core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::path_distance_
mutableprivate
bool const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::verbose_
private

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