#include <RNA_DMS_Potential.hh>

Inheritance diagram for core::scoring::rna::data::RNA_DMS_Potential:

Public Member Functions
	RNA_DMS_Potential ()

	~RNA_DMS_Potential () override

void	initialize (core::pose::Pose const &pose)

core::Real	evaluate (core::pose::Pose const &pose, pose::rna::RNA_Reactivity const &rna_reactivity)

Real	get_binding_energy (Size const i, core::Vector const &probe_xyz, core::scoring::ScoreFunction const &scorefxn)

Real	get_N1_lonepair_donor_angle (core::conformation::Residue const &acc_rsd, core::conformation::Residue const &don_rsd, Size const don_h_atm) const

bool	check_hbonded (pose::Pose const &pose, Size const &i, std::string const &atom_name, bool is_acceptor) const

bool	check_chbonded (pose::Pose const &pose, Size const &i, std::string const &atom_name) const

core::Vector	get_probe_xyz (core::conformation::Residue const &rsd, Distance const probe_dist) const

core::scoring::ScoreFunctionOP	get_probe_scorefxn (bool const soft_rep, bool const just_atr_rep) const

void	get_occupancy_densities (utility::vector1< Real > &occupancy_densities, pose::Pose const &pose, Size const i, core::Vector const &probe_xyz, utility::vector1< Distance > const &shells) const

Real	get_occupancy_density (pose::Pose const &pose, Size const i, core::Vector const &probe_xyz, std::pair< Distance, Distance > const &shells) const

utility::vector1< Real >	get_logL_values (pose::Pose const &pose, Size const i)

std::set< Real > const &	DMS_values () const

Private Member Functions
void	initialize_DMS_potential ()

numeric::MathNTensor< Real, 3 >	read_DMS_stats_file (std::string const &potential_file)

void	figure_out_potential ()

bool	get_features (pose::Pose const &pose, Size const i, bool &ade_n1_bonded, Real &binding_energy, Real &occupancy_density)

void	add_probe_to_pose (pose::Pose &pose)

void	update_virtual_base_if_necessary (pose::Pose &pose, Size const i)

Private Attributes
numeric::interpolation::InterpolatedPotential< 4 >	interpolated_potential_

bool const	separate_scores_

core::Distance	occ_dist_

core::Distance	methyl_probe_dist_

core::Distance	oxygen_probe_dist_

std::pair< Distance, Distance >	occ_shells_

std::set< Real >	is_bonded_values_

std::set< Real >	occ_values_

std::set< Real >	binding_energy_values_

std::set< Real >	DMS_values_

numeric::MathNTensor< Real, 4 >	DMS_stats_

numeric::MathTensor< Real >	p_model_

numeric::MathVector< Real >	p_DMS_

numeric::MathNTensor< Real, 4 >	DMS_potential_

numeric::MathMatrix< Real >	DMS_potential_is_bonded_

numeric::MathMatrix< Real >	DMS_potential_occ_

numeric::MathMatrix< Real >	DMS_potential_binding_energy_

core::pose::PoseOP	working_pose_

core::pose::PoseOP	working_pose_with_probe_

hbonds::HBondSetOP	hbond_set_

core::scoring::ScoreFunctionOP	probe_scorefxn_

Constructor & Destructor Documentation

◆ RNA_DMS_Potential()

core::scoring::rna::data::RNA_DMS_Potential::RNA_DMS_Potential ( )

References get_probe_scorefxn(), and probe_scorefxn_.

◆ ~RNA_DMS_Potential()

core::scoring::rna::data::RNA_DMS_Potential::~RNA_DMS_Potential ( )

overridedefault

Member Function Documentation

◆ add_probe_to_pose()

void core::scoring::rna::data::RNA_DMS_Potential::add_probe_to_pose ( pose::Pose & pose )

private

References core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueTypeBase::mode(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), and core::pose::Pose::size().

Referenced by initialize().

◆ check_chbonded()

bool core::scoring::rna::data::RNA_DMS_Potential::check_chbonded	(	pose::Pose const &	pose,
		Size const &	i,
		std::string const &	atom_name
	)		const

References core::conformation::Residue::atom_index(), protocols::buns::energy, core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), get_N1_lonepair_donor_angle(), core::conformation::Residue::Hpos_apolar(), core::scoring::carbon_hbonds::CarbonHBondEnergy::max_dis2(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by get_features().

◆ check_hbonded()

bool core::scoring::rna::data::RNA_DMS_Potential::check_hbonded	(	pose::Pose const &	pose,
		Size const &	i,
		std::string const &	atom_name,
		bool	is_acceptor
	)		const

References core::chemical::ResidueType::atom_name(), core::scoring::hbond, hbond_set_, and core::pose::Pose::residue_type().

Referenced by get_features().

◆ DMS_values()

std::set< Real > const& core::scoring::rna::data::RNA_DMS_Potential::DMS_values ( ) const

inline

References DMS_values_.

◆ evaluate()

Real core::scoring::rna::data::RNA_DMS_Potential::evaluate	(	core::pose::Pose const &	pose,
		pose::rna::RNA_Reactivity const &	rna_reactivity
	)

References binding_energy_values_, core::pose::full_model_info::const_full_model_info(), core::pose::rna::DMS, DMS_potential_, DMS_potential_binding_energy_, DMS_potential_is_bonded_, DMS_potential_occ_, DMS_values_, core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::FullModelInfo::full_to_sub(), get_features(), core::scoring::rna::data::get_idx(), core::conformation::Residue::has_variant_type(), initialize_DMS_potential(), interpolated_potential_, occ_values_, core::pack::dunbrack::polycubic_interpolation(), core::pose::rna::RNA_Reactivity::position(), core::chemical::REPLONLY, core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue(), protocols::hybridization::score, separate_scores_, core::pose::rna::RNA_Reactivity::type(), core::pose::rna::RNA_Reactivity::value(), core::chemical::VIRTUAL_RNA_RESIDUE, and core::pose::full_model_info::FullModelInfo::working_res().

Referenced by core::energy_methods::RNA_ChemicalMappingEnergy::calculate_energy().

◆ figure_out_potential()

void core::scoring::rna::data::RNA_DMS_Potential::figure_out_potential ( )

private

References binding_energy_values_, core::chemical::rna::DELTA, DMS_potential_, DMS_potential_binding_energy_, DMS_potential_is_bonded_, DMS_potential_occ_, DMS_stats_, DMS_values_, interpolated_potential_, is_bonded_values_, occ_values_, p_DMS_, p_model_, core::scoring::pcs, and protocols::hybridization::val.

Referenced by initialize_DMS_potential().

◆ get_binding_energy()

Real core::scoring::rna::data::RNA_DMS_Potential::get_binding_energy	(	Size const	i,
		core::Vector const &	probe_xyz,
		core::scoring::ScoreFunction const &	scorefxn
	)

References core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), update_virtual_base_if_necessary(), working_pose_, working_pose_with_probe_, and core::conformation::Residue::xyz().

Referenced by get_features().

◆ get_features()

bool core::scoring::rna::data::RNA_DMS_Potential::get_features	(	pose::Pose const &	pose,
		Size const	i,
		bool &	ade_n1_bonded,
		Real &	binding_energy,
		Real &	occupancy_density
	)

private

References core::conformation::Residue::aa(), check_chbonded(), check_hbonded(), core::pose::Pose::chi(), get_binding_energy(), get_occupancy_density(), get_probe_xyz(), methyl_probe_dist_, core::chemical::na_rad, occ_dist_, occ_shells_, oxygen_probe_dist_, probe_scorefxn_, and core::pose::Pose::residue().

Referenced by evaluate(), and get_logL_values().

◆ get_logL_values()

utility::vector1< Real > core::scoring::rna::data::RNA_DMS_Potential::get_logL_values	(	pose::Pose const &	pose,
		Size const	i
	)

References core::pose::Pose::aa(), binding_energy_values_, DMS_stats_, DMS_values_, get_features(), core::scoring::rna::data::get_idx(), core::chemical::na_rad, occ_values_, p_DMS_, p_model_, working_pose_, and working_pose_with_probe_.

◆ get_N1_lonepair_donor_angle()

Real core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle	(	core::conformation::Residue const &	acc_rsd,
		core::conformation::Residue const &	don_rsd,
		Size const	don_h_atm
	)		const

References core::conformation::Residue::aa(), core::conformation::Residue::has(), core::chemical::na_rad, protocols::hybridization::u, and core::conformation::Residue::xyz().

Referenced by check_chbonded().

◆ get_occupancy_densities()

void core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_densities	(	utility::vector1< Real > &	occupancy_densities,
		pose::Pose const &	pose,
		Size const	i,
		core::Vector const &	probe_xyz,
		utility::vector1< Distance > const &	shells
	)		const

References core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by get_occupancy_density().

◆ get_occupancy_density()

Real core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_density	(	pose::Pose const &	pose,
		Size const	i,
		core::Vector const &	probe_xyz,
		std::pair< Distance, Distance > const &	shells
	)		const