#include <MgKnowledgeBasedPotential.hh>

Inheritance diagram for core::scoring::magnesium::MgKnowledgeBasedPotential:

Public Member Functions
	MgKnowledgeBasedPotential ()
	ctor, reads data file More...

core::chemical::rna::GaussianParameter	get_mg_potential_gaussian_parameter (core::conformation::Residue const &rsd, Size const j, bool &is_phosphate_oxygen) const

core::chemical::rna::GaussianParameter	get_mg_potential_gaussian_parameter (core::conformation::Residue const &rsd, Size const j) const

core::chemical::rna::GaussianParameter	get_mg_potential_indirect_gaussian_parameter (core::conformation::Residue const &rsd, Size const j) const

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

core::chemical::rna::GaussianParameter	get_mg_potential_costheta_gaussian_parameter (core::conformation::Residue const &rsd, Size const j) const

core::chemical::rna::GaussianParameter	get_mg_potential_costheta_indirect_gaussian_parameter (core::conformation::Residue const &rsd, Size const j) const

core::Real	v_angle_width () const

Private Attributes
core::chemical::rna::GaussianParameter const	gaussian_parameter_phosphate_oxygen_

core::chemical::rna::GaussianParameter const	gaussian_parameter_imine_

core::chemical::rna::GaussianParameter const	gaussian_parameter_exocyclic_oxygen_

core::chemical::rna::GaussianParameter const	gaussian_parameter_o2prime_

core::chemical::rna::GaussianParameter const	gaussian_parameter_water_oxygen_

core::chemical::rna::GaussianParameter const	gaussian_parameter_phosphate_p_

core::chemical::rna::GaussianParameter const	gaussian_parameter_polar_H_

core::chemical::rna::GaussianParameter const	gaussian_parameter_nonpolar_H_

core::chemical::rna::GaussianParameter const	gaussian_parameter_phosphate_oxygen_indirect_

core::chemical::rna::GaussianParameter const	gaussian_parameter_imine_indirect_

core::chemical::rna::GaussianParameter const	gaussian_parameter_exocyclic_oxygen_indirect_

core::chemical::rna::GaussianParameter const	gaussian_parameter_o2prime_indirect_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_phosphate_oxygen_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_imine_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_exocyclic_oxygen_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_o2prime_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_water_oxygen_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_polar_H_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_nonpolar_H_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_phosphate_oxygen_indirect_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_imine_indirect_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_exocyclic_oxygen_indirect_

core::chemical::rna::GaussianParameter const	gaussian_parameter_costheta_o2prime_indirect_

Real const	v_angle_width_

Constructor & Destructor Documentation

◆ MgKnowledgeBasedPotential()

core::scoring::magnesium::MgKnowledgeBasedPotential::MgKnowledgeBasedPotential ( )

ctor, reads data file

ctor

Member Function Documentation

◆ get_mg_potential_costheta_gaussian_parameter()

core::chemical::rna::GaussianParameter core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter	(	core::conformation::Residue const &	rsd,
		Size const	j
	)		const

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), gaussian_parameter_costheta_exocyclic_oxygen_, gaussian_parameter_costheta_imine_, gaussian_parameter_costheta_nonpolar_H_, gaussian_parameter_costheta_o2prime_, gaussian_parameter_costheta_phosphate_oxygen_, gaussian_parameter_costheta_polar_H_, gaussian_parameter_costheta_water_oxygen_, and core::chemical::AtomType::name().

◆ get_mg_potential_costheta_indirect_gaussian_parameter()

core::chemical::rna::GaussianParameter core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter	(	core::conformation::Residue const &	rsd,
		Size const	j
	)		const

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), gaussian_parameter_costheta_exocyclic_oxygen_indirect_, gaussian_parameter_costheta_imine_indirect_, gaussian_parameter_costheta_o2prime_indirect_, gaussian_parameter_costheta_phosphate_oxygen_indirect_, and core::chemical::AtomType::name().

◆ get_mg_potential_gaussian_parameter() [1/2]

core::chemical::rna::GaussianParameter core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter	(	core::conformation::Residue const &	rsd,
		Size const	j
	)		const

References get_mg_potential_gaussian_parameter().

◆ get_mg_potential_gaussian_parameter() [2/2]

core::chemical::rna::GaussianParameter core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter	(	core::conformation::Residue const &	rsd,
		Size const	j,
		bool &	is_phosphate_oxygen
	)		const

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), gaussian_parameter_exocyclic_oxygen_, gaussian_parameter_imine_, gaussian_parameter_nonpolar_H_, gaussian_parameter_o2prime_, gaussian_parameter_phosphate_oxygen_, gaussian_parameter_phosphate_p_, gaussian_parameter_polar_H_, gaussian_parameter_water_oxygen_, core::conformation::Residue::is_RNA(), and core::chemical::AtomType::name().

Referenced by get_mg_potential_gaussian_parameter(), and setup_info_for_mg_calculation().

◆ get_mg_potential_indirect_gaussian_parameter()

core::chemical::rna::GaussianParameter core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter	(	core::conformation::Residue const &	rsd,
		Size const	j
	)		const

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), gaussian_parameter_exocyclic_oxygen_indirect_, gaussian_parameter_imine_indirect_, gaussian_parameter_o2prime_indirect_, gaussian_parameter_phosphate_oxygen_indirect_, gaussian_parameter_water_oxygen_, core::conformation::Residue::is_RNA(), and core::chemical::AtomType::name().

◆ setup_info_for_mg_calculation()

void core::scoring::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation ( core::pose::Pose & pose ) const

References core::pose::Pose::annotated_sequence(), core::chemical::rna::GaussianParameter::center, get_mg_potential_gaussian_parameter(), core::conformation::Residue::is_RNA(), core::scoring::rna::RNA_ScoringInfo::mg_calculation_annotated_sequence(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::scoring::rna::RNA_ScoringInfo::nonconst_atom_numbers_for_mg_calculation(), core::scoring::rna::RNA_ScoringInfo::nonconst_is_magnesium(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::set_mg_calculation_annotated_sequence(), and core::pose::Pose::size().

Referenced by protocols::magnesium::MgScanner::scan_magnesiums().

◆ v_angle_width()

core::Real core::scoring::magnesium::MgKnowledgeBasedPotential::v_angle_width ( ) const

inline

References v_angle_width_.

Member Data Documentation

◆ gaussian_parameter_costheta_exocyclic_oxygen_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_exocyclic_oxygen_

private

Referenced by get_mg_potential_costheta_gaussian_parameter().

◆ gaussian_parameter_costheta_exocyclic_oxygen_indirect_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_exocyclic_oxygen_indirect_

private

Referenced by get_mg_potential_costheta_indirect_gaussian_parameter().

◆ gaussian_parameter_costheta_imine_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_imine_

private

Referenced by get_mg_potential_costheta_gaussian_parameter().

◆ gaussian_parameter_costheta_imine_indirect_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_imine_indirect_

private

Referenced by get_mg_potential_costheta_indirect_gaussian_parameter().

◆ gaussian_parameter_costheta_nonpolar_H_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_nonpolar_H_

private

Referenced by get_mg_potential_costheta_gaussian_parameter().

◆ gaussian_parameter_costheta_o2prime_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_o2prime_

private

Referenced by get_mg_potential_costheta_gaussian_parameter().

◆ gaussian_parameter_costheta_o2prime_indirect_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_o2prime_indirect_

private

Referenced by get_mg_potential_costheta_indirect_gaussian_parameter().

◆ gaussian_parameter_costheta_phosphate_oxygen_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_phosphate_oxygen_

private

Referenced by get_mg_potential_costheta_gaussian_parameter().

◆ gaussian_parameter_costheta_phosphate_oxygen_indirect_

core::chemical::rna::GaussianParameter const core::scoring::magnesium::MgKnowledgeBasedPotential::gaussian_parameter_costheta_phosphate_oxygen_indirect_

private

Referenced by get_mg_potential_costheta_indirect_gaussian_parameter().