core::scoring::magnesium Namespace Reference

Classes
class	MgKnowledgeBasedPotential

Typedefs
typedef utility::pointer::shared_ptr < MgKnowledgeBasedPotential >	MgKnowledgeBasedPotentialOP
typedef utility::pointer::shared_ptr < MgKnowledgeBasedPotential const >	MgKnowledgeBasedPotentialCOP

Functions
Real	get_cos_theta (core::conformation::Residue const &rsd1, Size const i, Vector const &j_xyz, Size const i_base)
Real	get_cos_theta (core::conformation::Residue const &rsd1, Size const i, Vector const &j_xyz, Size &i_base, Vector &xyz_base)
Real	get_gaussian_potential_score (GaussianParameter const &mg_potential_gaussian_parameter, Vector const &pos1, Vector const &pos2)
Real	get_gaussian_score (GaussianParameter const &mg_potential_gaussian_parameter, Real const &d)
Real	get_gaussian_deriv (GaussianParameter const &mg_potential_gaussian_parameter, Real const &d)
void	get_closest_orbital_axis (core::conformation::Residue const &mg_rsd, Vector const &j_xyz, Size &which_orbital_atom, Real &cos_angle)
Real	get_cos_angle_to_closest_orbital_axis (core::conformation::Residue const &mg_rsd, Vector const &j_xyz)
Size	get_closest_orbital_axis (core::conformation::Residue const &mg_rsd, Vector const &j_xyz)

Typedef Documentation

typedef utility::pointer::shared_ptr< MgKnowledgeBasedPotential const > core::scoring::magnesium::MgKnowledgeBasedPotentialCOP

typedef utility::pointer::shared_ptr< MgKnowledgeBasedPotential > core::scoring::magnesium::MgKnowledgeBasedPotentialOP

Function Documentation

void core::scoring::magnesium::get_closest_orbital_axis	(	core::conformation::Residue const &	mg_rsd,
		Vector const &	j_xyz,
		Size &	which_orbital_atom,
		Real &	cos_angle
	)

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

Referenced by protocols::magnesium::MgMonteCarlo::apply(), and core::energy_methods::MgEnergy::eval_mg_interaction().

Size core::scoring::magnesium::get_closest_orbital_axis	(	core::conformation::Residue const &	mg_rsd,
		Vector const &	j_xyz
	)

Referenced by get_cos_angle_to_closest_orbital_axis().

Real core::scoring::magnesium::get_cos_angle_to_closest_orbital_axis	(	core::conformation::Residue const &	mg_rsd,
		Vector const &	j_xyz
	)

References get_closest_orbital_axis().

Referenced by core::energy_methods::MgEnergy::eval_mg_interaction().

Real core::scoring::magnesium::get_cos_theta	(	core::conformation::Residue const &	rsd1,
		Size const	i,
		Vector const &	j_xyz,
		Size const	i_base
	)

References get_cos_theta().

Referenced by core::energy_methods::MgEnergy::eval_mg_interaction(), and core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way().

Real core::scoring::magnesium::get_cos_theta	(	core::conformation::Residue const &	rsd1,
		Size const	i,
		Vector const &	j_xyz,
		Size &	i_base,
		Vector &	xyz_base
	)

References core::pose::motif::a(), core::conformation::Residue::abase2(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), protocols::match::upstream::b, core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::AtomType::hybridization(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), core::chemical::AtomType::name(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by get_cos_theta().

Real core::scoring::magnesium::get_gaussian_deriv	(	GaussianParameter const &	mg_potential_gaussian_parameter,
		Real const &	d
	)

References core::pose::motif::a(), core::chemical::rna::GaussianParameter::amplitude, core::chemical::rna::GaussianParameter::center, protocols::hybridization::d0, and core::chemical::rna::GaussianParameter::width.

Referenced by core::energy_methods::MgEnergy::eval_mg_interaction().

Real core::scoring::magnesium::get_gaussian_potential_score	(	GaussianParameter const &	mg_potential_gaussian_parameter,
		Vector const &	pos1,
		Vector const &	pos2
	)

References get_gaussian_score().

Referenced by core::energy_methods::MgEnergy::eval_mg_interaction(), and core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way().

Real core::scoring::magnesium::get_gaussian_score	(	GaussianParameter const &	mg_potential_gaussian_parameter,
		Real const &	d
	)

References core::pose::motif::a(), core::chemical::rna::GaussianParameter::amplitude, core::chemical::rna::GaussianParameter::center, protocols::hybridization::d0, protocols::hybridization::score, and core::chemical::rna::GaussianParameter::width.

Referenced by core::energy_methods::MgEnergy::eval_mg_interaction(), get_gaussian_potential_score(), and core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way().