core::scoring::rna::data::RNA_DMS_Potential Class Reference

#include <RNA_DMS_Potential.hh>

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

Public Member Functions
	RNA_DMS_Potential ()
	~RNA_DMS_Potential ()
void	initialize (core::pose::Pose const &pose)
core::Real	evaluate (core::pose::Pose const &pose, 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)
utility::vector1< Real > const &	DMS_values () const

Private Member Functions
void	initialize_DMS_potential ()
utility::vector1 < utility::vector1 < utility::vector1< core::Real > > >	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
bool const	separate_scores_
core::Distance	occ_dist_
core::Distance	methyl_probe_dist_
core::Distance	oxygen_probe_dist_
std::pair< Distance, Distance >	occ_shells_
utility::vector1< bool >	is_bonded_values_
utility::vector1< Real >	occ_values_
utility::vector1< Real >	binding_energy_values_
utility::vector1< Real >	DMS_values_
utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1< Real > > > >	DMS_stats_
utility::vector1 < utility::vector1 < utility::vector1< Real > > >	p_model_
utility::vector1< Real >	p_DMS_
utility::vector1 < utility::vector1 < utility::vector1 < utility::vector1< Real > > > >	DMS_potential_
utility::vector1 < utility::vector1< Real > >	DMS_potential_is_bonded_
utility::vector1 < utility::vector1< Real > >	DMS_potential_occ_
utility::vector1 < utility::vector1< 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

core::scoring::rna::data::RNA_DMS_Potential::RNA_DMS_Potential

(

)

References get_probe_scorefxn(), and probe_scorefxn_.

core::scoring::rna::data::RNA_DMS_Potential::~RNA_DMS_Potential

(

)

Member Function Documentation

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::ResidueTypeSet::name3_map(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), and core::pose::Pose::total_residue().

Referenced by initialize().

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(), 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::total_residue(), and core::conformation::Residue::xyz().

Referenced by get_features().

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().

utility::vector1< Real > const& core::scoring::rna::data::RNA_DMS_Potential::DMS_values ( ) const

inline

References DMS_values_.

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

References binding_energy_values_, core::pose::full_model_info::const_full_model_info(), core::scoring::rna::data::DMS, DMS_potential_, DMS_potential_binding_energy_, DMS_potential_is_bonded_, DMS_potential_occ_, DMS_values_, core::scoring::rna::data::get_bool_idx(), get_features(), core::scoring::rna::data::get_idx(), initialize_DMS_potential(), is_bonded_values_, occ_values_, core::scoring::rna::data::RNA_Reactivity::position(), separate_scores_, core::scoring::rna::data::RNA_Reactivity::type(), and core::scoring::rna::data::RNA_Reactivity::value().

Referenced by core::scoring::rna::data::RNA_ChemicalMappingEnergy::calculate_energy().

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

private

References binding_energy_values_, DMS_potential_, DMS_potential_binding_energy_, DMS_potential_is_bonded_, DMS_potential_occ_, DMS_stats_, DMS_values_, is_bonded_values_, occ_values_, p_DMS_, and p_model_.

Referenced by initialize_DMS_potential().

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::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), update_virtual_base_if_necessary(), working_pose_, working_pose_with_probe_, and core::conformation::Residue::xyz().

Referenced by 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().

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_, core::scoring::rna::data::get_bool_idx(), get_features(), core::scoring::rna::data::get_idx(), is_bonded_values_, core::chemical::na_rad, occ_values_, p_DMS_, p_model_, working_pose_, and working_pose_with_probe_.

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, and core::conformation::Residue::xyz().

Referenced by check_chbonded().

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::total_residue(), and core::conformation::Residue::xyz().

Referenced by 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

References get_occupancy_densities().

Referenced by get_features().

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

References core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_stack, core::scoring::FA_STANDARD_SOFT, core::scoring::geom_sol_fast, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbond_sc, core::scoring::lk_nonpolar, and core::scoring::hbonds::HBondOptions::use_hb_env_dep().

Referenced by RNA_DMS_Potential().

core::Vector core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz	(	core::conformation::Residue const &	rsd,
		Distance const	probe_dist
	)		const

References core::conformation::Residue::has(), core::conformation::Residue::name1(), and core::conformation::Residue::xyz().

Referenced by get_features().

void core::scoring::rna::data::RNA_DMS_Potential::initialize

(

core::pose::Pose const &

pose

)

References add_probe_to_pose(), core::pose::Pose::clone(), DMS_potential_, core::scoring::hbonds::fill_hbond_set(), hbond_set_, initialize_DMS_potential(), working_pose_, and working_pose_with_probe_.

Referenced by core::scoring::rna::data::RNA_ChemicalMappingEnergy::calculate_energy().

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

private

References DMS_stats_, figure_out_potential(), is_bonded_values_, and read_DMS_stats_file().

Referenced by evaluate(), and initialize().

vector1< vector1< vector1< Real > > > core::scoring::rna::data::RNA_DMS_Potential::read_DMS_stats_file ( std::string const &  potential_file )

private

References binding_energy_values_, core::scoring::rna::data::DMS, DMS_values_, core::scoring::rna::data::lookup_idx(), occ_values_, and core::io::serialization::size().

Referenced by initialize_DMS_potential().

void core::scoring::rna::data::RNA_DMS_Potential::update_virtual_base_if_necessary ( pose::Pose &  pose, Size const  i  )

private

References core::pose::add_variant_type_to_pose_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::total_residue(), and core::chemical::VIRTUAL_BASE.

Referenced by get_binding_energy().

Member Data Documentation

utility::vector1< Real > core::scoring::rna::data::RNA_DMS_Potential::binding_energy_values_

private

Referenced by evaluate(), figure_out_potential(), get_logL_values(), and read_DMS_stats_file().

utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_

private

Referenced by evaluate(), figure_out_potential(), and initialize().

utility::vector1< utility::vector1< Real > > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_binding_energy_

private

Referenced by evaluate(), and figure_out_potential().

utility::vector1< utility::vector1< Real > > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_is_bonded_

private

Referenced by evaluate(), and figure_out_potential().

utility::vector1< utility::vector1< Real > > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_occ_

private

Referenced by evaluate(), and figure_out_potential().

utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > core::scoring::rna::data::RNA_DMS_Potential::DMS_stats_

private

Referenced by figure_out_potential(), get_logL_values(), and initialize_DMS_potential().

utility::vector1< Real > core::scoring::rna::data::RNA_DMS_Potential::DMS_values_

private

Referenced by DMS_values(), evaluate(), figure_out_potential(), get_logL_values(), and read_DMS_stats_file().

hbonds::HBondSetOP core::scoring::rna::data::RNA_DMS_Potential::hbond_set_

private

Referenced by check_hbonded(), and initialize().

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_Potential::is_bonded_values_

private

Referenced by evaluate(), figure_out_potential(), get_logL_values(), and initialize_DMS_potential().

core::Distance core::scoring::rna::data::RNA_DMS_Potential::methyl_probe_dist_

private

Referenced by get_features().

core::Distance core::scoring::rna::data::RNA_DMS_Potential::occ_dist_

private

Referenced by get_features().

std::pair< Distance, Distance > core::scoring::rna::data::RNA_DMS_Potential::occ_shells_

private

Referenced by get_features().

utility::vector1< Real > core::scoring::rna::data::RNA_DMS_Potential::occ_values_

private

Referenced by evaluate(), figure_out_potential(), get_logL_values(), and read_DMS_stats_file().

core::Distance core::scoring::rna::data::RNA_DMS_Potential::oxygen_probe_dist_

private

Referenced by get_features().

utility::vector1< Real > core::scoring::rna::data::RNA_DMS_Potential::p_DMS_

private

Referenced by figure_out_potential(), and get_logL_values().

utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::rna::data::RNA_DMS_Potential::p_model_

private

Referenced by figure_out_potential(), and get_logL_values().

core::scoring::ScoreFunctionOP core::scoring::rna::data::RNA_DMS_Potential::probe_scorefxn_

private

Referenced by get_features(), and RNA_DMS_Potential().

bool const core::scoring::rna::data::RNA_DMS_Potential::separate_scores_

private

Referenced by evaluate().

core::pose::PoseOP core::scoring::rna::data::RNA_DMS_Potential::working_pose_

private

Referenced by get_binding_energy(), get_logL_values(), and initialize().

core::pose::PoseOP core::scoring::rna::data::RNA_DMS_Potential::working_pose_with_probe_

private

Referenced by get_binding_energy(), get_logL_values(), and initialize().

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

• src/core/scoring/rna/data/RNA_DMS_Potential.hh
• src/core/scoring/rna/data/RNA_DMS_Potential.cc