hbonds.cc File Reference

#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/constants.hh>
#include <core/scoring/hbonds/HBEvalTuple.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds_geom.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/conformation/Residue.hh>
#include <utility/graph/Graph.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/ScoreType.hh>
#include <basic/Tracer.hh>
#include <core/scoring/func/SmoothStepFunc.hh>
#include <core/scoring/Membrane_FAPotential.hh>
#include <core/scoring/MembranePotential.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/membrane/MembraneInfo.hh>
#include <core/conformation/membrane/MembraneGeometry.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/hydrate.OptionKeys.gen.hh>
#include <map>

Namespaces
	core
	A class for reading in the atom type properties.
	core::scoring
	core::scoring::hbonds

Functions
static basic::Tracer	core::scoring::hbonds::tr ("core.scoring.hbonds.hbonds")
bool	core::scoring::hbonds::residue_near_water (pose::Pose const &pose, Size ii)
	Waters ///. More...
core::Size	core::scoring::hbonds::next_hb_res (core::scoring::hbonds::HBond const &c_hb, core::Size const res)
	Get the residue that this residue connects to through this particular hbond We treat hbonds as directed connections (we ignore donor/acceptor). More...
void	core::scoring::hbonds::find_hb_paths (HBondSet const &local_hb_set, utility::vector1< core::Size > const &bridge_residues, std::map< std::string, core::Size > &paths, core::Size const current_res, core::Size const max_depth, std::string const &current_path, core::Size const current_depth, HBondCOP prev_hb)
	Recursive function to find all unique HBond paths involving bridge_residues and ending with a residue that is not in our bridged_residue list. More...
void	core::scoring::hbonds::fill_hbond_set (pose::Pose const &pose, bool const calculate_derivative, HBondSet &hbond_set, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc)
void	core::scoring::hbonds::fill_hbond_set (pose::Pose const &pose, bool const calculate_derivative, HBondSet &hbond_set, SSWeightParameters const &sswt, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc)
bool	core::scoring::hbonds::calculate_intra_res_hbonds (conformation::Residue const &rsd, HBondOptions const &options)
	General Utilities ///. More...
void	core::scoring::hbonds::fill_intra_res_hbond_set (pose::Pose const &pose, bool const calculate_derivative, HBondSet &hbond_set, bool const exclude_bb=false, bool const exclude_bsc=false, bool const exclude_scb=false, bool const exclude_sc=false)
	HBondSet Filling (Deprecated in favor of direct hbset functions)///. More...
core::Real	core::scoring::hbonds::get_ssdep_weight (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, SSWeightParameters const &ssdep)
void	core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold (pose::Pose const &pose, Real const AHdist_threshold, HBondSet &hbond_set)
	Fill HBondSet using the distance between the acceptor and hydrogen atoms as the definitional cutoff. Do not exclude any contacts and do not evaluate derivatives. More...
void	core::scoring::hbonds::identify_hbonds_1way (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_don_bb, bool const exclude_don_bsc, bool const exclude_acc_scb, bool const exclude_acc_sc, HBondSet &hbond_set, Real ssdep_weight_factor=1.0, bool bond_near_wat=false)
	HBond Database ///. More...
void	core::scoring::hbonds::identify_hbonds_1way (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc, HBondOptions const &options, EnergyMap &emap, Real ssdep_weight_factor, bool bond_near_wat)
void	core::scoring::hbonds::identify_hbonds_1way (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc, HBondOptions const &options, EnergyMap &emap, boost::unordered_map< core::Size, core::Size > &num_hbonds, Real ssdep_weight_factor, bool bond_near_wat)
Real	core::scoring::hbonds::hb_energy (HBondDatabase const &database, HBondOptions const &options, HBondSet const &hbset, conformation::Residue const &acc_rsd, Size aatm, conformation::Residue const &don_rsd, Size hatm)
	Returns the energy for the hydrogen bond between a given don/acceptor pair. More...
void	core::scoring::hbonds::identify_hbonds_1way_AHdist (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, Real const AHdist_threshold, HBondSet &hbond_set, bool bond_near_wat)
void	core::scoring::hbonds::identify_intra_res_hbonds (HBondDatabase const &database, conformation::Residue const &rsd, Size const rsd_nb, bool const evaluate_derivative, HBondSet &hbond_set, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc)
void	core::scoring::hbonds::identify_intra_res_hbonds (HBondDatabase const &database, conformation::Residue const &rsd, Size const rsd_nb, HBondOptions const &options, EnergyMap &emap)
void	core::scoring::hbonds::increment_hbond_energy (HBEvalType const &hbe_type, EnergyMap &emap, Real hbE)
	Scoring ///. More...
void	core::scoring::hbonds::increment_npd_hbond_energy (HBEvalType const &hbe_type, EnergyMap &emap, Real hbE, bool intra_res)
	Increment the appropriate places in the input energy map for a particular hydrogen bond. More...
void	core::scoring::hbonds::get_hbond_energies (HBondSet const &hbond_set, EnergyMap &emap)
Real	core::scoring::hbonds::hb_eval_type_weight (HBEvalType const &hbe_type, EnergyMap const &weights, bool const intra_res, bool const put_intra_into_total)
Real	core::scoring::hbonds::npd_hb_eval_type_weight (HBEvalType const &hbe_type, EnergyMap const &weights, bool const intra_res, bool const put_intra_into_total)
core::Real	core::scoring::hbonds::burial_weight (int const nb)
core::Real	core::scoring::hbonds::hb_env_dep_burial_lin (int const nb1, int const nb2)
void	core::scoring::hbonds::burial3class_weight_initializer (FArray2D_double &burial)
int	core::scoring::hbonds::get_burial_3 (int const neighbors, int const threshold_1, int const threshold_3)
core::Real	core::scoring::hbonds::hb_env_dep_burial_tk (int const nb1, int const nb2)
Real	core::scoring::hbonds::get_environment_dependent_weight (HBEvalTuple const &hbe_type, int const don_nb, int const acc_nb, HBondOptions const &options)
bool	core::scoring::hbonds::nonzero_hbond_weight (ScoreFunction const &scorefxn)
void	core::scoring::hbonds::identify_hbonds_1way_membrane (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_don_bb, bool const exclude_don_bsc, bool const exclude_acc_scb, bool const exclude_acc_sc, HBondSet &hbond_set, pose::Pose const &pose, bool bond_near_wat=false)
	Identify Membrane Hydrogen Bonds (Env) More...
void	core::scoring::hbonds::identify_hbonds_1way_membrane (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc, HBondOptions const &options, EnergyMap &emap, pose::Pose const &pose, bool bond_near_wat)
Real	core::scoring::hbonds::get_membrane_depth_dependent_weight (pose::Pose const &pose, int const don_nb, int const acc_nb, int const Hrsd, int const Arsd, int const Hatm, int const Aatm, Vector const &Hxyz, Vector const &Axyz)
Real	core::scoring::hbonds::get_membrane_depth_dependent_weight (Vector const &normal, Vector const &center, Real const &thickness, Real const &steepness, int const don_nb, int const acc_nb, Vector const &Hxyz, Vector const &Axyz)

Detailed Description

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